Capsid protein p24
Human immunodeficiency virus 1
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count | Chain A； UniProt 133–363 | Not recorded | Cleavage and polyadenylation specificity factor subunit 6 × 6 （Q16630） IHP INOSITOL HEXAKISPHOSPHATE × 12 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.3M Calcium chloride dihydrate, 0.3 M Magnesium chloride hexahydrate, 0.1 M Tris hydrochloride pH 8.5, 0.1 M Bicine, 20% PEG 4000 | Resolution 2.93 Å R-free 0.336 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 7ZUD | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1A43 STRUCTURE OF THE HIV-1 CAPSID PROTEIN DIMERIZATION DOMAIN AT 2.6A RESOLUTION Deposited 1998-02-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
277–362（86 aa）
Fragment：C-TERMINAL DOMAIN OF HIV-1 CAPSID PROTEIN RESIDUES 146-231 (CAPSID NUMBERING)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5；pH 5.0
|
Resolution 2.60 Å R-free 0.281 |
| 1A8O HIV CAPSID C-TERMINAL DOMAIN Deposited 1998-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
283–351（69 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 151 - 231
|
Mutation：SELENOMETHIONINE SUBSTITUTIONS, L151MSE, M185MSE, M214MSE, M215MSE Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；CRYSTALS OF CA(151-231) WERE GROWN AT 4C IN 4 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (2.1 MM CA(151-231) IN 10MM TRIS (PH 8.0) AND 2 MM 2-MERCAPTOETHANOL) AND RESERVOIR SOLUTION (2.0 M AMMONIUM SULFATE), vapor diffusion - sitting drop, temperature 277K
|
Resolution 1.70 Å R-free 0.253 |
| 1AFV HIV-1 CAPSID PROTEIN (P24) COMPLEX WITH FAB25.3 Deposited 1997-03-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
132–282（151 aa）
Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 151
Chain B
132–282（151 aa）
Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 151
|
Not recorded | PB LEAD (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；16% PEG 3350, 50 MM BISTRIS-HCL, PH 7.0, 0.1% BETA-OCTYLGLUCOSIDE, 1 MM NAN3
|
Resolution 3.70 Å R-free 0.324 |
| 1AK4 HUMAN CYCLOPHILIN A BOUND TO THE AMINO-TERMINAL DOMAIN OF HIV-1 CAPSID Deposited 1997-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
132–276（145 aa）
Fragment：N-TERMINAL DOMAIN
|
Mutation：DELETION MUTANT DEL(152-231) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；THE PROTEIN SOLUTION WAS 0.25 MM CYPA AND 0.25 MM CA(151) IN 10 MM TRISHCL (PH 8.0) AND 1 MM 2-MERCAPTOETHANOL. THE RESERVOIR SOLUTION WAS 1ML OF 1.0 M LICL, 0.1 M BICINE (PH 7.0), AND 22% POLYETHYLENE GLYCOL 8000. THE INITIAL DROP WAS 6 MICROL OF A 1:1 MIX OF PROTEIN AND RESERVOIR SOLUTIONS.
|
Resolution 2.36 Å R-free 0.306 |
| 1AK4 HUMAN CYCLOPHILIN A BOUND TO THE AMINO-TERMINAL DOMAIN OF HIV-1 CAPSID Deposited 1997-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
132–276（145 aa）
Fragment：N-TERMINAL DOMAIN
|
Mutation：DELETION MUTANT DEL(152-231) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；THE PROTEIN SOLUTION WAS 0.25 MM CYPA AND 0.25 MM CA(151) IN 10 MM TRISHCL (PH 8.0) AND 1 MM 2-MERCAPTOETHANOL. THE RESERVOIR SOLUTION WAS 1ML OF 1.0 M LICL, 0.1 M BICINE (PH 7.0), AND 22% POLYETHYLENE GLYCOL 8000. THE INITIAL DROP WAS 6 MICROL OF A 1:1 MIX OF PROTEIN AND RESERVOIR SOLUTIONS.
|
Resolution 2.36 Å R-free 0.306 |
| 1AUM HIV CAPSID C-TERMINAL DOMAIN (CAC146) Deposited 1997-08-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
282–351（70 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 146 - 231
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；CRYSTALS OF CAC(146-231) WERE GROWN AT 4C IN 8 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (2.1 MM CA(151-231) IN 10 MM TRIS (PH 8.0) AND 2 MM 2-MERCAPTOETHANOL) AND RESERVOIR SOLUTION (2.0 M AMMONIUM SULFATE), vapor diffusion - sitting drop
|
Resolution 3.00 Å |
| 1B92 MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WITH CATALYTIC ACTIVITY Deposited 1999-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
765–927（163 aa）
Fragment：CATALYTIC CORE DOMAIN
|
Mutation：F185K, G149A | CAC CACODYLATE ION × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.02 Å R-free 0.289 |
| 1B92 MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WITH CATALYTIC ACTIVITY Deposited 1999-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
765–927（163 aa）
Fragment：CATALYTIC CORE DOMAIN
|
Mutation：F185K, G149A | CAC CACODYLATE ION × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.02 Å R-free 0.289 |
| 1B9D MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WITH CATALYTIC ACTIVITY Deposited 1999-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
765–927（163 aa）
Fragment：CATALYTIC CORE DOMAIN
|
Mutation：F185K | CAC CACODYLATE ION × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 1.70 Å R-free 0.278 |
| 1B9D MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WITH CATALYTIC ACTIVITY Deposited 1999-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
765–927（163 aa）
Fragment：CATALYTIC CORE DOMAIN
|
Mutation：F185K | CAC CACODYLATE ION × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 1.70 Å R-free 0.278 |
| 1B9F MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WITH CATALYTIC ACTIVITY Deposited 1999-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
765–927（163 aa）
Fragment：CATALYTIC CORE DOMAIN
|
Mutation：F185K, G140A, G149A | CAC CACODYLATE ION × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 1.70 Å R-free 0.280 |
| 1B9F MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WITH CATALYTIC ACTIVITY Deposited 1999-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
765–927（163 aa）
Fragment：CATALYTIC CORE DOMAIN
|
Mutation：F185K, G140A, G149A | CAC CACODYLATE ION × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 1.70 Å R-free 0.280 |
| 1BAJ HIV-1 CAPSID PROTEIN C-TERMINAL FRAGMENT PLUS GAG P2 DOMAIN Deposited 1998-04-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
275–376（102 aa）
Fragment：C-TERMINAL DOMAIN OF HIV-1 CAPSID PROTEIN (RESIDUES 146-229 CAPSID NUMBERING) FOLLOWED BY THE 14 AMINO ACID P2 DOMAIN OF GAG
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5；pH 5.0
|
Resolution 2.60 Å R-free 0.275 |
| 1BHL CACODYLATED CATALYTIC DOMAIN OF HIV-1 INTEGRASE Deposited 1998-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
772–922（151 aa）
Fragment：CATALYTIC CORE DOMAIN, RESIDUES 50 - 212
|
Mutation：F185H Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；3-9% PEG 8000, 0.4M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE PH 6.5
|
Resolution 2.20 Å R-free 0.264 |
| 1BI4 CATALYTIC DOMAIN OF HIV-1 INTEGRASE Deposited 1998-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1196–1355（160 aa）
Fragment：CATALYTIC CORE DOMAIN 50 - 212
Chain B
1196–1355（160 aa）
Fragment：CATALYTIC CORE DOMAIN 50 - 212
Chain C
1196–1355（160 aa）
Fragment：CATALYTIC CORE DOMAIN 50 - 212
|
Mutation：F185H Mutation：F185H Mutation：F185H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；435 MM SODIUM CITRATE, 50 MM HEPES-HCL, PH 7.5, 7.5 MM DTT, PROTEIN CONCENTRATION, 0.13 MM
|
Resolution 2.50 Å R-free 0.271 |
| 1BIS HIV-1 INTEGRASE CORE DOMAIN Deposited 1998-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
762–924（163 aa）
Fragment：CORE DOMAIN
Chain B
762–924（163 aa）
Fragment：CORE DOMAIN
|
Mutation：W131E, F185K Mutation：W131E, F185K | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 100 MM HEPES, PH 7.0, 5 MM DTT
|
Resolution 1.95 Å R-free 0.256 |
| 1BIU HIV-1 INTEGRASE CORE DOMAIN COMPLEXED WITH MG++ Deposited 1998-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
762–927（166 aa）
Fragment：CORE DOMAIN
Chain B
762–927（166 aa）
Fragment：CORE DOMAIN
|
Mutation：W131E, F185K Mutation：W131E, F185K | MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 100 MM HEPES, PH 7.0, 5 MM DTT, 5 MM MGCL2
|
Resolution 2.50 Å R-free 0.265 |
| 1BIU HIV-1 INTEGRASE CORE DOMAIN COMPLEXED WITH MG++ Deposited 1998-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
762–927（166 aa）
Fragment：CORE DOMAIN
|
Mutation：W131E, F185K | MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 100 MM HEPES, PH 7.0, 5 MM DTT, 5 MM MGCL2
|
Resolution 2.50 Å R-free 0.265 |
| 1BL3 CATALYTIC DOMAIN OF HIV-1 INTEGRASE Deposited 1998-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
765–924（160 aa）
Fragment：CATALYTIC CORE DOMAIN 50 - 212
Chain B
765–924（160 aa）
Fragment：CATALYTIC CORE DOMAIN 50 - 212
Chain C
765–924（160 aa）
Fragment：CATALYTIC CORE DOMAIN 50 - 212
|
Mutation：F185H Mutation：F185H Mutation：F185H | MG MAGNESIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；435MM SODIUM CITRATE, 50MM HEPES-HCL PH 7.5, 7.5MM DTT, [PROTEIN]=0.13MM
|
Resolution 2.00 Å R-free 0.279 |
| 1ITG CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HIV-1 INTEGRASE: SIMILARITY TO OTHER POLYNUCLEOTIDYL TRANSFERASES Deposited 1994-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
762–927（166 aa）
|
Not recorded | CAC CACODYLATE ION × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 1WJB SOLUTION STRUCTURE OF THE N-TERMINAL ZN BINDING DOMAIN OF HIV-1 INTEGRASE (D FORM), NMR, 40 STRUCTURES Deposited 1997-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
716–770（55 aa）
Chain B
716–770（55 aa）
|
Not recorded | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7.4；293 K
|
Resolution not provided |
| 1WJD SOLUTION STRUCTURE OF THE N-TERMINAL ZN BINDING DOMAIN OF HIV-1 INTEGRASE (E FORM), NMR, 38 STRUCTURES Deposited 1997-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
716–770（55 aa）
Chain B
716–770（55 aa）
|
Not recorded | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7.4；293 K
|
Resolution not provided |
| 20XX HIV-1 integrase core domain in complex with potent allosteric inhibitors Deposited 2025-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1MCX (2~{S})-2-[(3~{a}~{R},7~{a}~{R})-1'-ethyl-5'-methyl-spiro[1,3,3~{a},4,5,6,7,7~{a}-octahydroindene-2,3'-indene]-4'-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 1PE PENTAETHYLENE GLYCOL × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1 M sodium cacodylate, 0.2 M ammonium sulfate, 20% (w/v) PEG8000, 25% (w/v) PEG 200 and 5 mM DTT solution and flash-frozen in liquid nitrogen.
|
Resolution 2.20 Å R-free 0.251 |
| 2B4J Structural basis for the recognition between HIV-1 integrase and LEDGF/p75 Deposited 2005-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
765–927（163 aa）
Fragment：HIV-1 integrase
Chain B
765–927（163 aa）
Fragment：HIV-1 integrase
|
Mutation：F185K Mutation：F185K | PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.25；295 K；PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.02 Å R-free 0.226 |
| 2B4J Structural basis for the recognition between HIV-1 integrase and LEDGF/p75 Deposited 2005-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
765–927（163 aa）
Fragment：HIV-1 integrase
Chain B
765–927（163 aa）
Fragment：HIV-1 integrase
|
Mutation：F185K Mutation：F185K | PO4 PHOSPHATE ION × 4 GOL GLYCEROL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.25；295 K；PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.02 Å R-free 0.226 |
| 2GOL Xray Structure of Gag278 Deposited 2006-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–131（131 aa）
Fragment：residues 1-131
Chain B
132–277（146 aa）
Fragment：N-terminal Domain (residues 132-277)
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.7；294 K；28% PEG 8000, 0.2 M (NH4)2SO4, 0.1 M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 2.20 Å R-free 0.258 |
| 2GOL Xray Structure of Gag278 Deposited 2006-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
132–277（146 aa）
Fragment：N-terminal Domain (residues 132-277)
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.7；294 K；28% PEG 8000, 0.2 M (NH4)2SO4, 0.1 M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 2.20 Å R-free 0.258 |
| 2GON Xray Structure of Gag133-278 Deposited 2006-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
132–277（146 aa）
Fragment：N-terminal Domain (residues 133-278)
|
Mutation：A224E Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；286 K；0.2 M BiAmmonium Citrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K
|
Resolution 1.90 Å R-free 0.257 |
| 2GON Xray Structure of Gag133-278 Deposited 2006-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
132–277（146 aa）
Fragment：N-terminal Domain (residues 133-278)
|
Mutation：A224E Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；286 K；0.2 M BiAmmonium Citrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K
|
Resolution 1.90 Å R-free 0.257 |
| 2GON Xray Structure of Gag133-278 Deposited 2006-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
132–277（146 aa）
Fragment：N-terminal Domain (residues 133-278)
|
Mutation：A224E Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；286 K；0.2 M BiAmmonium Citrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K
|
Resolution 1.90 Å R-free 0.257 |
| 2GON Xray Structure of Gag133-278 Deposited 2006-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
132–277（146 aa）
Fragment：N-terminal Domain (residues 133-278)
|
Mutation：A224E Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；286 K；0.2 M BiAmmonium Citrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K
|
Resolution 1.90 Å R-free 0.257 |
| 2H3F Solution structure of the HIV-1 MA protein Deposited 2006-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–131（131 aa）
Fragment：residues 2-132
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5.5；308 K；Pressure ambient
NMR sample composition
50mM phosphate buffer, 5mM DTT, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2H3I Solution structure of the HIV-1 myristoylated Matrix protein Deposited 2006-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–131（131 aa）
Fragment：residues 2-132
|
Not recorded | MYR MYRISTIC ACID × 1 |
SOLUTION NMR
NMR measurement conditions
pH 5.5；308 K；Pressure ambient
NMR sample composition
50mM phosphate buffer, 5mM DTT, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2H3Q Solution structure of HIV-1 myrMA bound to di-C4-phosphatidylinositol-(4,5)-bisphosphate Deposited 2006-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–131（131 aa）
Fragment：residues 2-132
|
Not recorded | MYR MYRISTIC ACID × 1 PBU (2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1 ,2-DIYL DIBUTANOATE × 1 |
SOLUTION NMR
NMR measurement conditions
pH 5.5；308 K；Pressure ambient
NMR sample composition
50mM phosphate buffer, 5mM DTT, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2H3V Structure of the HIV-1 Matrix protein bound to di-C8-phosphatidylinositol-(4,5)-bisphosphate Deposited 2006-05-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–131（131 aa）
Fragment：residues 2-132
|
Not recorded | PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 |
SOLUTION NMR
NMR measurement conditions
pH 5.5；308 K；Pressure ambient
NMR sample composition
50mM phosphate buffer, 5mM DTT, 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2H3Z Structure of the HIV-1 matrix protein bound to di-C4-phosphatidylinositol-(4,5)-bisphosphate Deposited 2006-05-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–131（131 aa）
Fragment：residues 2-132
|
Not recorded | PBU (2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1 ,2-DIYL DIBUTANOATE × 1 |
SOLUTION NMR
NMR measurement conditions
pH 5.5；308 K；Pressure ambient
NMR sample composition
50mM phosphate buffer, 5mM DTT, 10% H2O, 10% D2O | 10% H2O + 10% D2O
|
Resolution not provided |
| 2HMX HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 MATRIX PROTEIN Deposited 1995-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–131（131 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 2HVP THREE-DIMENSIONAL STRUCTURE OF ASPARTYL PROTEASE FROM HUMAN IMMUNODEFICIENCY VIRUS HIV-1 Deposited 1989-04-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
24–122（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 2ITG CATALYTIC DOMAIN OF HIV-1 INTEGRASE: ORDERED ACTIVE SITE IN THE F185H CONSTRUCT Deposited 1996-09-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
765–927（163 aa）
Fragment：CATALYTIC CORE DOMAIN 50 - 212
|
Mutation：F185H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；3-9% PEG 8000, 0.4M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE PH 6.5
|
Resolution 2.60 Å |
| 2JPR Joint refinement of the HIV-1 CA-NTD in complex with the assembly inhibitor CAP-1 Deposited 2007-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
133–277（145 aa）
Fragment：sequence database residues, 133-277
|
Not recorded | JPR 1-(3-chloro-4-methylphenyl)-3-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)thio]ethyl}urea × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；308 K；Ionic strength (raw mmCIF value) 25；Pressure ambient
NMR sample composition
100-700 uM [U-15N] sodium phosphate, 100% D2O | 100% D2O
|
Resolution not provided |
| 2JYG Solution Structure of the W184A/M185A Mutant of the Carboxy-terminal Dimerization Domain of the HIV-1 Capsid Protein Deposited 2007-12-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
280–363（84 aa）
Fragment：residues 280-363
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5；303 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition
1 mM [U-98% 13C; U-98% 15N] Protein, 1 mM [U-98% 15N] Protein, 1 mM [U-95% 13C] Protein, 90% v/v H2O, 10% mM [U-100% 2H] D2O, 50 mM sodium phosphate, 90%H2o/10%D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2JYL Solution Structure of A Double Mutant of The Carboxy-terminal Dimerization Domain of The HIV-1 Capsid Protein Deposited 2007-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
280–363（84 aa）
|
Mutation：W184A, M185A | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5；303 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition
1 mM [U-98% 13C; U-98% 15N] Protein, 50 mM sodium phosphate, 90%H2o/10%D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-98% 15N] Protein, 50 mM sodium phosphate, 90%H2o/10%D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-95% 13C] Protein, 50 mM sodium phosphate, 90%H2o/10%D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-98% 13C; U-98% 15N] Protein, 50 mM sodium phosphate, 100%D2O | 100% D2O
NMR sample composition
1 mM [U-98% 15N] Protein, 50 mM sodium phosphate, 100%D2O | 100% D2O
NMR sample composition
1 mM [U-95% 13C] Protein, 50 mM sodium phosphate, 100%D2O | 100% D2O
|
Resolution not provided |
| 2LYA Structure of HIV-1 myr(-) matrix protein in complex with 1,2-dioctanoyl-sn-phosphatidylcholine Deposited 2012-09-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–132（131 aa）
|
Not recorded | PC8 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 |
SOLUTION NMR
NMR measurement conditions
pH 5.5；308 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition
0.4 mM [U-95% 13C] MA, 0.8-1.0 mM 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 50 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.4-1.0 mM [U-95% 13C; U-95% 15N] MA, 0.8-1.0 mM 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 50 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2LYB Structure of HIV-1 myr(-) matrix protein in complex with 1,2-dioctanoyl-sn-phosphatidyl-L-serine Deposited 2012-09-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–132（131 aa）
|
Not recorded | 8SP O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 |
SOLUTION NMR
NMR measurement conditions
pH 5.5；308 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition
0.4 mM [U-95% 13C] MA, 0.8-1.0 mM 1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt, 50 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.4-1.0 mM [U-95% 13C; U-95% 15N] MA, 0.8-1.0 mM 1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt, 50 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2M3Z NMR solution structure of HIV-1 nucleocapsid protein in complex with an inhibitor displaying a 2 inhibitors:1 NC stoichiometry Deposited 2013-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
378–432（55 aa）
|
Not recorded | ZN ZINC ION × 2 1HF (3E)-3-{(2Z)-[(5Z)-5-(furan-2-ylmethylidene)-4-oxo-1,3-thiazolidin-2-ylidene]hydrazinylidene}-2-oxo-2,3-dihydro-1H-indole-5-sulfonic acid × 2 |
SOLUTION NMR
NMR measurement conditions
pH 6.5；300 K；Ionic strength (raw mmCIF value) 0.025；Pressure ambient
NMR sample composition
250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2M8L HIV capsid dimer structure Deposited 2013-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
133–363（231 aa）
Chain B
133–363（231 aa）
|
Not recorded | No recorded non-water small molecule |
Experimental method not declared
NMR measurement conditions
pH 6.5；308 K；Pressure ambient
NMR sample composition
0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2M8N HIV-1 capsid monomer structure Deposited 2013-05-24 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
133–363（231 aa）
|
Not recorded | No recorded non-water small molecule |
Experimental method not declared
NMR measurement conditions
pH 6.5；308 K；Pressure ambient
NMR sample composition
0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2M8P The structure of the W184AM185A mutant of the HIV-1 capsid protein Deposited 2013-05-24 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
133–363（231 aa）
|
Mutation：W184A, M185A | No recorded non-water small molecule |
Experimental method not declared
NMR measurement conditions
pH 6.5；308 K；Pressure ambient
NMR sample composition
0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2ONT A swapped dimer of the HIV-1 capsid C-terminal domain Deposited 2007-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
277–352（76 aa）
Fragment：capsid C-terminal domain, residues 278-353
|
Mutation：deletion of Ala177 | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.75；277 K；Reservoir: 0.1 M Sodium phosphate pH 6.75, 28% v/v PEG 1500, 15% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.294 |
| 2PWM Crystal Structure of HIV-1 CA146 A92E real cell Deposited 2007-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
133–278（146 aa）
Fragment：N-Terminal Domain
Chain B
133–278（146 aa）
Fragment：N-Terminal Domain
|
Mutation：A92E Mutation：A92E | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；24% PEG 4500, 0.60 M MgCl2, and 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.270 |
| 2PWM Crystal Structure of HIV-1 CA146 A92E real cell Deposited 2007-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
133–278（146 aa）
Fragment：N-Terminal Domain
Chain D
133–278（146 aa）
Fragment：N-Terminal Domain
|
Mutation：A92E Mutation：A92E | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；24% PEG 4500, 0.60 M MgCl2, and 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.270 |
| 2PWM Crystal Structure of HIV-1 CA146 A92E real cell Deposited 2007-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
133–278（146 aa）
Fragment：N-Terminal Domain
Chain F
133–278（146 aa）
Fragment：N-Terminal Domain
|
Mutation：A92E Mutation：A92E | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；24% PEG 4500, 0.60 M MgCl2, and 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.270 |
| 2PWM Crystal Structure of HIV-1 CA146 A92E real cell Deposited 2007-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
133–278（146 aa）
Fragment：N-Terminal Domain
Chain H
133–278（146 aa）
Fragment：N-Terminal Domain
|
Mutation：A92E Mutation：A92E | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；24% PEG 4500, 0.60 M MgCl2, and 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.270 |
| 2PWO Crystal Structure of HIV-1 CA146 A92E Psuedo Cell Deposited 2007-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
133–278（146 aa）
Fragment：N-Terminal Domain
Chain B
133–278（146 aa）
Fragment：N-Terminal Domain
|
Mutation：A92E Mutation：A92E | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；24% PEG 4500, 0.60 M MgCl2, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.45 Å R-free 0.216 |
| 2PWO Crystal Structure of HIV-1 CA146 A92E Psuedo Cell Deposited 2007-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
133–278（146 aa）
Fragment：N-Terminal Domain
Chain D
133–278（146 aa）
Fragment：N-Terminal Domain
|
Mutation：A92E Mutation：A92E | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；24% PEG 4500, 0.60 M MgCl2, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.45 Å R-free 0.216 |
| 2PXR Crystal Structure of HIV-1 CA146 in the Presence of CAP-1 Deposited 2007-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
133–278（146 aa）
Fragment：N-Terminal Domain
|
Not recorded | CL CHLORIDE ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；286 K；100 mM Tris pH, 5% PEG 8000, 20% PEG 300, 10% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K
|
Resolution 1.50 Å R-free 0.221 |
| 2PXR Crystal Structure of HIV-1 CA146 in the Presence of CAP-1 Deposited 2007-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
133–278（146 aa）
Fragment：N-Terminal Domain
|
Not recorded | CL CHLORIDE ION × 2 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；286 K；100 mM Tris pH, 5% PEG 8000, 20% PEG 300, 10% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K
|
Resolution 1.50 Å R-free 0.221 |
| 2PXR Crystal Structure of HIV-1 CA146 in the Presence of CAP-1 Deposited 2007-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
133–278（146 aa）
Fragment：N-Terminal Domain
|
Not recorded | CL CHLORIDE ION × 2 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；286 K；100 mM Tris pH, 5% PEG 8000, 20% PEG 300, 10% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K
|
Resolution 1.50 Å R-free 0.221 |
| 2XV6 Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 220) in complex with a camelid VHH. Deposited 2010-10-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
278–352（75 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-352
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
30% PEG 4000
|
Resolution 1.89 Å R-free 0.195 |
| 2XV6 Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 220) in complex with a camelid VHH. Deposited 2010-10-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
278–352（75 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-352
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
30% PEG 4000
|
Resolution 1.89 Å R-free 0.195 |
| 2XXM Crystal structure of the HIV-1 capsid protein C-terminal domain in complex with a camelid VHH and the CAI peptide. Deposited 2010-11-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
278–352（75 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-352
|
Not recorded | ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
30% PEG4000, 200MM AMMONIUM ACETATE, 100MM SODIUM ACETATE PH 4.6
|
Resolution 1.65 Å R-free 0.217 |
| 3AV9 Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 ACY ACETIC ACID × 4 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.70 Å R-free 0.202 |
| 3AVA Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 1 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.70 Å R-free 0.200 |
| 3AVB Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 3 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.85 Å R-free 0.194 |
| 3AVC Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.77 Å R-free 0.196 |
| 3AVF Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1356（160 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1356（160 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 ACY ACETIC ACID × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.70 Å R-free 0.199 |
| 3AVG Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.70 Å R-free 0.203 |
| 3AVH Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.88 Å R-free 0.200 |
| 3AVI Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 1 ACY ACETIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.70 Å R-free 0.194 |
| 3AVJ Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 ACY ACETIC ACID × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.70 Å R-free 0.198 |
| 3AVK Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 ACY ACETIC ACID × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP
|
Resolution 1.75 Å R-free 0.199 |
| 3AVL Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.88 Å R-free 0.194 |
| 3AVM Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 ACY ACETIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.88 Å R-free 0.197 |
| 3AVN Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site Deposited 2011-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
Chain B
1197–1359（163 aa）
Fragment：CCD domain (UNP RESIDUES 1197-1359)
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 2.10 Å R-free 0.205 |
| 3DIK Pseudo-atomic model of the HIV-1 CA hexameric lattice Deposited 2008-06-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
133–351（219 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON CRYSTALLOGRAPHY
cryo-EM buffer
17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate；pH 6.5；17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate
cryo-EM vitrification conditions
Cryogen ETHANE；Washed with 0.1M KCl, blotted briefly, and plunged into liquid ethane
|
Resolution 9.00 Å |
| 3H47 X-ray Structure of Hexameric HIV-1 CA Deposited 2009-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
133–363（231 aa）
Fragment：UNP residues 133-363
|
Mutation：A14C,E45C,W184A,M185A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；10-12% PEG 8,000, 100 mM sodium malonate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.270 |
| 3H4E X-ray Structure of Hexameric HIV-1 CA Deposited 2009-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
133–363（231 aa）
Fragment：UNP residues 133-363
Chain B
133–363（231 aa）
Fragment：UNP residues 133-363
Chain C
133–363（231 aa）
Fragment：UNP residues 133-363
Chain D
133–363（231 aa）
Fragment：UNP residues 133-363
Chain E
133–363（231 aa）
Fragment：UNP residues 133-363
Chain F
133–363（231 aa）
Fragment：UNP residues 133-363
|
Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10-12% PEG 8,000, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.263 |
| 3H4E X-ray Structure of Hexameric HIV-1 CA Deposited 2009-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain G
133–363（231 aa）
Fragment：UNP residues 133-363
Chain H
133–363（231 aa）
Fragment：UNP residues 133-363
Chain I
133–363（231 aa）
Fragment：UNP residues 133-363
Chain J
133–363（231 aa）
Fragment：UNP residues 133-363
Chain K
133–363（231 aa）
Fragment：UNP residues 133-363
Chain L
133–363（231 aa）
Fragment：UNP residues 133-363
|
Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A Mutation：A14C,E45C,W184A,M185A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10-12% PEG 8,000, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.263 |
| 3MGE X-ray Structure of Hexameric HIV-1 CA Deposited 2010-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
133–363（231 aa）
Fragment：UNP residues 133-363
|
Mutation：A42C, T54C, W184A, M185A | EDO 1,2-ETHANEDIOL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10% PEG 8,000
2% Tacsimate
100 mM Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.255 |
| 3WNE Cyclic hexapeptide PKIDNG in complex with HIV-1 integrase Deposited 2013-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1203–1359（157 aa）
Fragment：Catalytic core domain, UNP residue 1203-1359
Chain B
1203–1359（157 aa）
Fragment：Catalytic core domain, UNP residue 1203-1359
|
Mutation：C56S, S123G, T124A, K127R, W131D, F139D, F185H Mutation：C56S, S123G, T124A, K127R, W131D, F139D, F185H | CD CADMIUM ION × 4 CL CHLORIDE ION × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8M AMMONIUM SULFATE, 0.15M SODIUM CITRATE, 5mM CADMIUM CHLORIDE , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.228 |
| 3WNF Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase Deposited 2013-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1203–1359（157 aa）
Fragment：Catalytic core domain, UNP residue 1203-1359
Chain B
1203–1359（157 aa）
Fragment：Catalytic core domain, UNP residue 1203-1359
|
Mutation：C56S, S123G, T124A, K127R, W131D, F139D, F185H Mutation：C56S, S123G, T124A, K127R, W131D, F139D, F185H | CD CADMIUM ION × 4 CL CHLORIDE ION × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8M AMMONIUM SULFATE, 0.15M SODIUM CITRATE, 5MM CADMIUM CHLORIDE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.45 Å R-free 0.232 |
| 3WNG Cyclic hexapeptide PKIDNp in complex with HIV-1 integrase Deposited 2013-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1203–1359（157 aa）
Fragment：Catalytic core domain, UNP residue 1203-1359
Chain B
1203–1359（157 aa）
Fragment：Catalytic core domain, UNP residue 1203-1359
|
Mutation：C56S, S123G, T124A, K127R, W131D, F139D, F185H Mutation：C56S, S123G, T124A, K127R, W131D, F139D, F185H | CD CADMIUM ION × 4 CL CHLORIDE ION × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8M Ammonium Sulfate, 0.15M Sodium Citrate, 5MM Cadmium Chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.75 Å R-free 0.222 |
| 3WNH Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase Deposited 2013-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1203–1359（157 aa）
Fragment：Catalytic core domain, UNP residue 1203-1359
Chain B
1203–1359（157 aa）
Fragment：Catalytic core domain, UNP residue 1203-1359
|
Mutation：C56S, S123G, T124A, K127R, W131D, F139D, F185H Mutation：C56S, S123G, T124A, K127R, W131D, F139D, F185H | CD CADMIUM ION × 4 CL CHLORIDE ION × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8M Ammonium Sulfate, 0.15M Sodium Citrate, 5MM Cadmium Chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.50 Å R-free 0.227 |
| 4AH9 Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification Deposited 2012-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1197-1359
Chain B
1197–1359（163 aa）
Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1197-1359
|
Mutation：YES Mutation：YES | 0MB 1-(3-PHENYL-1,2,4-THIADIAZOL-5-YL)-1,4-DIAZEPANE × 2 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 4 GOL GLYCEROL × 2 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；100 MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 M TO 1.5 M AMMONIUM SULFATE. THE PROTEIN WAS IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION.
|
Resolution 1.70 Å R-free 0.209 |
| 4AHR Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification Deposited 2012-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1197-1359
Chain B
1197–1359（163 aa）
Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1197-1359
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACY ACETIC ACID × 3 GOL GLYCEROL × 2 I2E 3-(1,3-benzodioxol-5-yl)propanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PROTEIN: 5.5MG/ML IN 40MM TRIS BUFFER AT PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT. CRYSTALLANT: 100MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 TO 1.5M AMMONIUM SULFATE AT 20C IN SITTING DROP PLATES. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION.
|
Resolution 1.90 Å R-free 0.234 |
| 4AHS Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification Deposited 2012-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1197-1359
Chain B
1197–1359（163 aa）
Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1197-1359
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACT ACETATE ION × 5 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 AKH 1-BENZOFURAN-7-CARBOXYLIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PROTEIN: 5.5MG/ML IN 40MM TRIS BUFFER AT PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT. CRYSTALLANT: 100MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 TO 1.5M AMMONIUM SULFATE AT 20C IN SITTING DROP PLATES. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION.
|
Resolution 1.75 Å R-free 0.248 |
| 4AHT Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification Deposited 2012-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
Fragment：INTEGRASE, RESIDUES 1197-1359
Chain B
1197–1359（163 aa）
Fragment：INTEGRASE, RESIDUES 1197-1359
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 2 Q6T 1,3-benzodioxole-4-carboxylic acid × 2 ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PROTEIN: 5.5MG/ML IN 40MM TRIS BUFFER AT PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT. CRYSTALLANT: 100MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 TO 1.5M AMMONIUM SULFATE AT 20C IN SITTING DROP PLATES. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION.
|
Resolution 1.80 Å R-free 0.198 |
| 4AHU Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification Deposited 2012-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
Fragment：INTEGRASE RESIDUES 1197-1359
Chain B
1197–1359（163 aa）
Fragment：INTEGRASE RESIDUES 1197-1359
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 GOL GLYCEROL × 4 ICO 1H-INDOLE-3-CARBOXYLIC ACID × 2 ACY ACETIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PROTEIN: 5.5MG/ML IN 40MM TRIS BUFFER AT PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT. CRYSTALLANT: 100MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 TO 1.5M AMMONIUM SULFATE AT 20C IN SITTING DROP PLATES. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION.
|
Resolution 1.90 Å R-free 0.198 |
| 4AHV Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification Deposited 2012-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1197-1359
Chain B
1197–1359（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1197-1359
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACY ACETIC ACID × 2 EDO 1,2-ETHANEDIOL × 5 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 2 Z5P 1-[2-(1H-pyrazol-1-yl)phenyl]methanamine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PROTEIN: 5.5MG/ML IN 40 MM TRIS BUFFER AT PH 8.0, 250 MM NACL, 30 MM MGCL2, 5MM DTT. CRYSTALLANT: 100 MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 TO 1.5 M AMMONIUM SULFATE AT 20C IN SITTING DROP PLATES. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION.
|
Resolution 1.80 Å R-free 0.224 |
| 4COC HIV-1 capsid C-terminal domain mutant (Y169L) Deposited 2014-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Mutation：YES | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；30% PEG 4000, 0.2 M LISO4, 0.1 M TRIS PH 8.5
|
Resolution 1.59 Å R-free 0.223 |
| 4COC HIV-1 capsid C-terminal domain mutant (Y169L) Deposited 2014-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；30% PEG 4000, 0.2 M LISO4, 0.1 M TRIS PH 8.5
|
Resolution 1.59 Å R-free 0.223 |
| 4COC HIV-1 capsid C-terminal domain mutant (Y169L) Deposited 2014-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Mutation：YES | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；30% PEG 4000, 0.2 M LISO4, 0.1 M TRIS PH 8.5
|
Resolution 1.59 Å R-free 0.223 |
| 4COP HIV-1 capsid C-terminal domain mutant (Y169S) Deposited 2014-01-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
Chain B
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Mutation：YES Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 10.5；1.2 M NAH2PO4, 0.8 M K2HPO4, 0.1 M CAPS PH 10.5 AND 0.2 M LISO4
|
Resolution 1.85 Å R-free 0.247 |
| 4DMN HIV-1 Integrase Catalytical Core Domain Deposited 2012-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1197–1359（163 aa）
|
Not recorded | ARS ARSENIC × 2 SO4 SULFATE ION × 2 0L9 (2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](methoxy)ethanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.5 K；10% PEG 8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulfate, Vapor Diffusion, hanging drop, temperature 277.5K
|
Resolution 2.45 Å R-free 0.276 |
| 4DMN HIV-1 Integrase Catalytical Core Domain Deposited 2012-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Not recorded | ARS ARSENIC × 4 SO4 SULFATE ION × 4 0L9 (2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](methoxy)ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.5 K；10% PEG 8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulfate, Vapor Diffusion, hanging drop, temperature 277.5K
|
Resolution 2.45 Å R-free 0.276 |
| 4E1M Crystal Structure of HIV-1 Integrase with a non-catayltic site inhibitor Deposited 2012-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | TQ2 (2S)-tert-butoxy[4-(3,4-dimethylphenyl)-2-methylquinolin-3-yl]ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8% PEG 8000, 100mM NaCacodylate, 200mM ammonium sulfate, 5mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.273 |
| 4E1N Crystal Structure of HIV-1 Integrase with a non-catayltic site inhibitor Deposited 2012-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | TQX (2S)-tert-butoxy[4-(8-fluoro-5-methyl-3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8% PEG 8000, 100mM NaCacodylate, 200mM ammonium sulfate, 5mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.265 |
| 4GVM HIV-1 Integrase Catalytic Core Domain A128T Mutant Complexed with Allosteric Inhibitor Deposited 2012-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
Fragment：UNP residues 1197-1359
|
Mutation：A128T | ARS ARSENIC × 4 LF2 (2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](tert-butoxy)ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Na Cacodylate, pH 6.5, 1.4 M Na Acetate, Vapor Diffusion,hanging drop, temperature 293K
|
Resolution 2.16 Å R-free 0.249 |
| 4GW6 HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor Deposited 2012-08-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
Fragment：UNP residues 1197-1359
|
Not recorded | ARS ARSENIC × 4 LF2 (2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](tert-butoxy)ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；277.5 K；10% PEG8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulphate, Vapor Diffusion, hanging drop, temperature 277.5K
|
Resolution 2.65 Å R-free 0.238 |
| 4ID1 HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor Deposited 2012-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | LF0 (2S)-tert-butoxy[4-(3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.5 K；10% PEG8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulphate, Vapor Diffusion,hanging drop, temperature 277.5K
|
Resolution 1.87 Å R-free 0.234 |
| 4IPY HIV capsid C-terminal domain Deposited 2013-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
Chain B
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
Chain C
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
Chain D
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；reservoir contained 0.2 M magnesium formate dihydrate (pH 7.0) and 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.64 Å R-free 0.218 |
| 4IPY HIV capsid C-terminal domain Deposited 2013-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；reservoir contained 0.2 M magnesium formate dihydrate (pH 7.0) and 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.64 Å R-free 0.218 |
| 4IPY HIV capsid C-terminal domain Deposited 2013-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；reservoir contained 0.2 M magnesium formate dihydrate (pH 7.0) and 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.64 Å R-free 0.218 |
| 4IPY HIV capsid C-terminal domain Deposited 2013-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；reservoir contained 0.2 M magnesium formate dihydrate (pH 7.0) and 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.64 Å R-free 0.218 |
| 4IPY HIV capsid C-terminal domain Deposited 2013-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
278–363（86 aa）
Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；reservoir contained 0.2 M magnesium formate dihydrate (pH 7.0) and 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.64 Å R-free 0.218 |
| 4JLH HIV-1 Integrase Catalytic Core Domain A128T Mutant Complexed with Allosteric Inhibitor Deposited 2013-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：A128T, F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | 0L9 (2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](methoxy)ethanoic acid × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Na Cacodylate, 1.4 M Na Acetate, pH 6.5, Vapor Diffusion, hanging drop, temperature 293K
|
Resolution 2.09 Å R-free 0.243 |
| 4JMU Crystal structure of HIV matrix residues 1-111 in complex with inhibitor Deposited 2013-03-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–111（111 aa）
Fragment：UNP residues 1-111
|
Not recorded | SO4 SULFATE ION × 1 1ML 5-{4-[(4-methoxybenzoyl)amino]phenoxy}-2-{[(trans-4-methylcyclohexyl)carbonyl](propan-2-yl)amino}benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；22.5% PEG2000MME, 100mM NaOAc pH4.5, 100mM Ammonium sulfate, 7.5% DMSO , VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.257 |
| 4LQW Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin Deposited 2013-07-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
133–278（146 aa）
Fragment：UNP Residues 133-278
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；23 % v/v PEG 4000, 23 % glycerol, 8.5 % isopropanol, 85 mM HEPES pH 7.5, 20 mM spermine tetrahydrochloride, 100 mM glycine, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 1.95 Å R-free 0.246 |
| 4LQW Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin Deposited 2013-07-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
133–278（146 aa）
Fragment：UNP Residues 133-278
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；23 % v/v PEG 4000, 23 % glycerol, 8.5 % isopropanol, 85 mM HEPES pH 7.5, 20 mM spermine tetrahydrochloride, 100 mM glycine, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 1.95 Å R-free 0.246 |
| 4NX4 Re-refinement of CAP-1 HIV-CA complex Deposited 2013-12-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
133–278（146 aa）
Fragment：HIV-1 CAPSID (UNP residues 133-278)
|
Not recorded | CL CHLORIDE ION × 1 ZN ZINC ION × 2 JPR 1-(3-chloro-4-methylphenyl)-3-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)thio]ethyl}urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；286 K；100 MM TRIS, 5% PEG 8000, 20% PEG 300, 10% GLYCEROL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K
|
Resolution 1.50 Å R-free 0.191 |
| 4O0J HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[4-(4-chlorophenyl)-6-(3,4-dimethylphenyl)-2,5-dimethylpyridin-3-yl]ethanoic acid Deposited 2013-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | LF8 (2S)-tert-butoxy[4-(4-chlorophenyl)-6-(3,4-dimethylphenyl)-2,5-dimethylpyridin-3-yl]ethanoic acid × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.5 K；10% PEG8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulphate, Vapor Diffusion,hanging drop, temperature 277.5K
|
Resolution 2.05 Å R-free 0.232 |
| 4O55 HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid Deposited 2013-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | LF9 (2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.5 K；10% PEG8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulphate, Vapor Diffusion,hanging drop, temperature 277.5K
|
Resolution 2.24 Å R-free 0.259 |
| 4O5B HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid Deposited 2013-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：A128T Non-standard monomer：Yes (specific site not provided by mmCIF) | LF9 (2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M Na Cacodylate, pH 6.5, 1.4 M Na Acetate, Vapor Diffusion,hanging drop, temperature 292K
|
Resolution 2.37 Å R-free 0.233 |
| 4PHV X-RAY CRYSTAL STRUCTURE OF THE HIV PROTEASE COMPLEX WITH L-700,417, AN INHIBITOR WITH PSEUDO C2 SYMMETRY Deposited 1991-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
24–122（99 aa）
Chain B
24–122（99 aa）
|
Not recorded | VAC N,N-BIS(2-HYDROXY-1-INDANYL)-2,6- DIPHENYLMETHYL-4-HYDROXY-1,7-HEPTANDIAMIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å |
| 4QNB Disulfide stabilized HIV-1 CA hexamer in complex with PHENYL-L-PHENYLALANINAMIDE inhibitor Deposited 2014-06-17 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
133–363（231 aa）
|
Mutation：A14C,E45C,W184A,M185A | 1B0 N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10% PEG 8,000, 2% Tacsimate, 100 mM Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.271 |
| 4WYM Structural basis of HIV-1 capsid recognition by CPSF6 Deposited 2014-11-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
133–363（231 aa）
Chain B
133–363（231 aa）
Chain C
133–363（231 aa）
Chain D
133–363（231 aa）
Chain E
133–363（231 aa）
Chain F
133–363（231 aa）
|
Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 M sodium formate, ammonium acetate, tri-sodium citrate, sodium/potassium tartrate, sodium oxamate; 0.1 M sodium HEPES, MOPS; 30% glycerol, PEG 4000
|
Resolution 2.60 Å R-free 0.259 |
| 4WYM Structural basis of HIV-1 capsid recognition by CPSF6 Deposited 2014-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric |
Chain G
133–363（231 aa）
Chain H
133–363（231 aa）
Chain I
133–363（231 aa）
Chain J
133–363（231 aa）
Chain K
133–363（231 aa）
Chain L
133–363（231 aa）
|
Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 M sodium formate, ammonium acetate, tri-sodium citrate, sodium/potassium tartrate, sodium oxamate; 0.1 M sodium HEPES, MOPS; 30% glycerol, PEG 4000
|
Resolution 2.60 Å R-free 0.259 |
| 5TEO Dimer of HIV-1 Gag CTD-SP1 fragment Deposited 2016-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
278–377（100 aa）
Chain B
278–377（100 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；290 K；20% PEG 3350, 0.1-0.2M dibasic ammonium phosphate
|
Resolution 2.05 Å R-free 0.244 |
| 5TEO Dimer of HIV-1 Gag CTD-SP1 fragment Deposited 2016-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
278–377（100 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；290 K；20% PEG 3350, 0.1-0.2M dibasic ammonium phosphate
|
Resolution 2.05 Å R-free 0.244 |
| 5TEO Dimer of HIV-1 Gag CTD-SP1 fragment Deposited 2016-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
278–377（100 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；290 K；20% PEG 3350, 0.1-0.2M dibasic ammonium phosphate
|
Resolution 2.05 Å R-free 0.244 |
| 6IK9 HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:dGTP ternary complex Deposited 2018-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C749S, C867S | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM Bis-Tris-HCl PH 6.0, 30-40 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 3.5-4% PEG 6000, 2.4% sucrose, 4.8% glycerol
|
Resolution 2.44 Å R-free 0.225 |
| 6IK9 HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:dGTP ternary complex Deposited 2018-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C749S, C867S | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM Bis-Tris-HCl PH 6.0, 30-40 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 3.5-4% PEG 6000, 2.4% sucrose, 4.8% glycerol
|
Resolution 2.44 Å R-free 0.225 |
| 6IKA HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:entecavir-triphosphate ternary complex Deposited 2018-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C749S, C867S | ET9 [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM Bis-Tris-HCl PH 6.0, 30-40 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 3.5-4% PEG 6000, 2.4% sucrose, 4.8% glycerol
|
Resolution 2.60 Å R-free 0.232 |
| 6IKA HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:entecavir-triphosphate ternary complex Deposited 2018-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C749S, C867S | ET9 [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM Bis-Tris-HCl PH 6.0, 30-40 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 3.5-4% PEG 6000, 2.4% sucrose, 4.8% glycerol
|
Resolution 2.60 Å R-free 0.232 |
| 6KDJ HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:lamivudine 5'-triphosphate ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C749S, C867S | 1RZ Lamivudine Triphosphate × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.51 Å R-free 0.230 |
| 6KDJ HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:lamivudine 5'-triphosphate ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C749S, C867S | 1RZ Lamivudine Triphosphate × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.51 Å R-free 0.230 |
| 6KDK HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dCTP ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C749S, C867S | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.56 Å R-free 0.234 |
| 6KDK HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dCTP ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C749S, C867S | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.56 Å R-free 0.234 |
| 6KDM HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir 5'-triphosphate ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C749S, C867S | GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 ET9 [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.32 Å R-free 0.223 |
| 6KDM HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir 5'-triphosphate ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C749S, C867S | GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 ET9 [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.32 Å R-free 0.223 |
| 6KDN HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dGTP ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C749S, C867S | MG MAGNESIUM ION × 1 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.30 Å R-free 0.221 |
| 6KDN HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dGTP ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C749S, C867S | MG MAGNESIUM ION × 1 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.30 Å R-free 0.221 |
| 6KDO HIV-1 reverse transcriptase with Q151M/Y115F/F116Y/M184V/F160M:DNA:lamivudine 5'-triphosphate ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C749S, C867S | GOL GLYCEROL × 2 1RZ Lamivudine Triphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.57 Å R-free 0.230 |
| 6KDO HIV-1 reverse transcriptase with Q151M/Y115F/F116Y/M184V/F160M:DNA:lamivudine 5'-triphosphate ternary complex Deposited 2019-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C749S, C867S | GOL GLYCEROL × 2 1RZ Lamivudine Triphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.57 Å R-free 0.230 |
| 6LMI Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-6-methanesulfonamido-2,3',4',5-tetramethyl-[1,1'-biphenyl]-4-yl]acetic acid Deposited 2019-12-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 4 PGE TRIETHYLENE GLYCOL × 2 EJ9 (2S)-2-[2-(3,4-dihydro-2H-chromen-6-yl)-4-(3,4-dimethylphenyl)-3,6-dimethyl-5-(methylsulfonylamino)phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1M Sodium cacodylate pH6.5, 0.32M Ammonium sulfate, 9% PEG 8000, 5mM DTT
|
Resolution 2.50 Å R-free 0.244 |
| 6LMQ Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-[3-(3,4-dihydro-2H-1,4-benzoxazin-6-yl)-6-methanesulfonamido-2,3',4',5-tetramethyl-[1,1'-biphenyl]-4-yl]acetic acid Deposited 2019-12-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 4 PGE TRIETHYLENE GLYCOL × 2 940 (2S)-2-[2-(3,4-dihydro-2H-1,4-benzoxazin-6-yl)-4-(3,4-dimethylphenyl)-3,6-dimethyl-5-(methylsulfonylamino)phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1M Sodium cacodylate pH6.5, 0.206M Ammonium sulfate, 1% PEG 8000, 5mM DTT
|
Resolution 2.10 Å R-free 0.239 |
| 7D83 Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-(2-(3-cyclohexylureido)-3,6-dimethyl-5-(5-methylchroman-6-yl)pyridin-4-yl)acetic acid Deposited 2020-10-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：F1332K Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 6 GZ9 (2S)-2-[2-(cyclohexylcarbamoylamino)-3,6-dimethyl-5-(5-methyl-3,4-dihydro-2H-chromen-6-yl)pyridin-4-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1M Sodium cacodylate pH 6.5, 0.2M Ammonium sulfate, 1% PEG 8000, 5mM DTT
|
Resolution 2.43 Å R-free 0.278 |
| 7DBM HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V:DNA:dGTP ternary complex Deposited 2020-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C749S,C867S | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.43 Å R-free 0.224 |
| 7DBM HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V:DNA:dGTP ternary complex Deposited 2020-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C749S,C867S | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.43 Å R-free 0.224 |
| 7DBN HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V/F160M:DNA:dCTP ternary complex Deposited 2020-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.67 Å R-free 0.225 |
| 7DBN HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V/F160M:DNA:dCTP ternary complex Deposited 2020-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL
|
Resolution 2.67 Å R-free 0.225 |
| 7WCE Crystal structure of HIV-1 integrase catalytic core domain in complex with (2S)-2-(tert-Butoxy)-2-(10-fluoro-2-(2-hydroxy-4-methylphenyl)-1,4-dimethyl-5-(methylsulfonyl)-5,6-dihydrophenanthridin-3-yl)acetic acid Deposited 2021-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1197–1359（163 aa）
|
Mutation：F1332K Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 8Z3 (2S)-2-[10-fluoranyl-1,4-dimethyl-2-(4-methyl-2-oxidanyl-phenyl)-5-methylsulfonyl-6H-phenanthridin-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1 M Sodium cacodylate pH 6.5, 0.23 M Ammonium sulfate, 6% PEG 8000, 5 mM DTT
|
Resolution 1.85 Å R-free 0.214 |
| 8A1P HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor BI-D Deposited 2022-06-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1367–1435（69 aa）
Chain A
1197–1359（163 aa）
Chain B
1367–1435（69 aa）
Chain B
1197–1359（163 aa）
Chain C
1367–1435（69 aa）
Chain C
1197–1359（163 aa）
Chain D
1367–1435（69 aa）
Chain D
1197–1359（163 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 5 GOL GLYCEROL × 2 LF0 (2S)-tert-butoxy[4-(3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, ethylene glycol, magnesium chloride, calcium chloride, Tris-Bicine
|
Resolution 1.80 Å R-free 0.209 |
| 8A1Q HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor STP0404 (Pirmitegravir) Deposited 2022-06-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1367–1435（69 aa）
Chain A
1197–1359（163 aa）
Chain B
1367–1435（69 aa）
Chain B
1197–1359（163 aa）
Chain C
1367–1435（69 aa）
Chain C
1197–1359（163 aa）
Chain D
1367–1435（69 aa）
Chain D
1197–1359（163 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 15 WBV (2S)-tert-butoxy{4-(4-chlorophenyl)-2,3,6-trimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole-MES
|
Resolution 2.06 Å R-free 0.235 |
| 8BUV HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3 Deposited 2022-11-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1367–1435（69 aa）
Chain A
1197–1359（163 aa）
Chain B
1367–1435（69 aa）
Chain B
1197–1359（163 aa）
Chain C
1367–1435（69 aa）
Chain C
1197–1359（163 aa）
Chain D
1367–1435（69 aa）
Chain D
1197–1359（163 aa）
|
Not recorded | MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 6 723 (6-chloro-2-oxo-4-phenyl-1,2-dihydroquinolin-3-yl)acetic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES
|
Resolution 2.04 Å R-free 0.247 |
| 8BV2 Biological and structural analysis of new potent Integrase-LEDGF allosteric HIV-1 inhibitors Deposited 2022-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | RWR (2S)-2-[3-cyclopropyl-2-(3,4-dihydro-2H-chromen-6-yl)-6-methyl-phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3 microliters of protein at 5 mg/mL in 50 mM MES pH5.5, 50 mM NaCl, 5 mM DTT mixed with 3 microliters of reservoir solution containing 0.1 M sodium cacodylate pH 6.5, 1.26 M ammonium sulfate.
|
Resolution 2.00 Å R-free 0.226 |
| 8CBR HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor BDM-2 Deposited 2023-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1367–1435（69 aa）
Chain A
1197–1359（163 aa）
Chain B
1367–1435（69 aa）
Chain B
1197–1359（163 aa）
Chain C
1367–1435（69 aa）
Chain C
1197–1359（163 aa）
Chain D
1367–1435（69 aa）
Chain D
1197–1359（163 aa）
|
Not recorded | RWR (2S)-2-[3-cyclopropyl-2-(3,4-dihydro-2H-chromen-6-yl)-6-methyl-phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 EDO 1,2-ETHANEDIOL × 14 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES
|
Resolution 1.80 Å R-free 0.211 |
| 8CBS HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT871 Deposited 2023-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1367–1435（69 aa）
Chain A
1197–1359（163 aa）
Chain B
1367–1435（69 aa）
Chain B
1197–1359（163 aa）
Chain C
1367–1435（69 aa）
Chain C
1197–1359（163 aa）
Chain D
1367–1435（69 aa）
Chain D
1197–1359（163 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 14 CL CHLORIDE ION × 1 U5L (2~{S})-2-[3-cyclopropyl-6-methyl-2-(5-methyl-3,4-dihydro-2~{H}-chromen-6-yl)phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES
|
Resolution 1.70 Å R-free 0.198 |
| 8CBT HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT872 Deposited 2023-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1367–1435（69 aa）
Chain A
1197–1359（163 aa）
Chain B
1367–1435（69 aa）
Chain B
1197–1359（163 aa）
Chain C
1367–1435（69 aa）
Chain C
1197–1359（163 aa）
Chain D
1367–1435（69 aa）
Chain D
1197–1359（163 aa）
|
Not recorded | W2Q (2~{S})-2-[3-cyclopropyl-2-(3,4-dihydro-2~{H}-chromen-6-yl)-6-methyl-phenyl]-2-cyclopropyloxy-ethanoic acid × 2 EDO 1,2-ETHANEDIOL × 5 MG MAGNESIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 4 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES
|
Resolution 2.14 Å R-free 0.253 |
| 8CBU HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT884 Deposited 2023-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1367–1435（69 aa）
Chain A
1197–1359（163 aa）
Chain B
1367–1435（69 aa）
Chain B
1197–1359（163 aa）
Chain C
1367–1435（69 aa）
Chain C
1197–1359（163 aa）
Chain D
1367–1435（69 aa）
Chain D
1197–1359（163 aa）
|
Not recorded | CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 7 U60 (2S)-2-[3-cyclopropyl-6-methyl-2-(5-methyl-3,4-dihydro-2H-chromen-6-yl)phenyl]-2-cyclopropyloxy-ethanoic acid × 2 MG MAGNESIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES
|
Resolution 2.44 Å R-free 0.254 |
| 8CBV HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT916 Deposited 2023-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1367–1435（69 aa）
Chain A
1197–1359（163 aa）
Chain B
1367–1435（69 aa）
Chain B
1197–1359（163 aa）
Chain C
1367–1435（69 aa）
Chain C
1197–1359（163 aa）
Chain D
1367–1435（69 aa）
Chain D
1197–1359（163 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 10 PEG DI(HYDROXYETHYL)ETHER × 1 U5S (2~{S})-2-[3-cyclopropyl-2-(8-fluoranyl-5-methyl-3,4-dihydro-2~{H}-chromen-6-yl)-6-methyl-phenyl]-2-cyclopropyloxy-ethanoic acid × 2 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES
|
Resolution 1.82 Å R-free 0.230 |
| 8F22 HIV-CA Disulfide linked Hexamer bound to 11l capsid inhibitor. Deposited 2022-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
133–356（224 aa）
Chain B
133–356（224 aa）
Chain C
133–356（224 aa）
Chain D
133–356（224 aa）
Chain E
133–356（224 aa）
Chain F
133–356（224 aa）
|
Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A | XBQ Nalpha-{[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]acetyl}-N-(4-methoxyphenyl)-N-methyl-L-phenylalaninamide × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291.15 K；0.2 M Calcium acetate hydrate, 100 mM sodium cacodylate pH 6.5, 40% w/v PEG300, 0.500 mM 11l, and previous crystal seed solution.
|
Resolution 2.50 Å R-free 0.347 |
| 8F22 HIV-CA Disulfide linked Hexamer bound to 11l capsid inhibitor. Deposited 2022-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain G
133–356（224 aa）
Chain H
133–356（224 aa）
Chain I
133–356（224 aa）
Chain J
133–356（224 aa）
Chain K
133–356（224 aa）
Chain L
133–356（224 aa）
|
Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291.15 K；0.2 M Calcium acetate hydrate, 100 mM sodium cacodylate pH 6.5, 40% w/v PEG300, 0.500 mM 11l, and previous crystal seed solution.
|
Resolution 2.50 Å R-free 0.347 |
| 8FN7 Structure of WT HIV-1 intasome bound to Dolutegravir Deposited 2022-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Not recorded | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8FND Structure of E138K HIV-1 intasome with Dolutegravir bound Deposited 2022-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：E138K Mutation：E138K Mutation：E138K Mutation：E138K Mutation：E138K Mutation：E138K Mutation：E138K Mutation：E138K | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8FNG Structure of G140A HIV-1 intasome with Dolutegravir bound Deposited 2022-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：G140A Mutation：G140A Mutation：G140A Mutation：G140A Mutation：G140A Mutation：G140A Mutation：G140A Mutation：G140A | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å |
| 8FNH Structure of Q148K HIV-1 intasome with Dolutegravir bound Deposited 2022-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：Q148K Mutation：Q148K Mutation：Q148K Mutation：Q148K Mutation：Q148K Mutation：Q148K Mutation：Q148K Mutation：Q148K | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 8FNJ Structure of E138K/G140A HIV-1 intasome with Dolutegravir bound Deposited 2022-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: 12-meric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：E138K,G140A Mutation：E138K,G140A Mutation：E138K,G140A Mutation：E138K,G140A Mutation：E138K,G140A Mutation：E138K,G140A Mutation：E138K,G140A Mutation：E138K,G140A | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 8FNL Structure of E138K/Q148K HIV-1 intasome with Dolutegravir bound Deposited 2022-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：E138K,Q148K Mutation：E138K,Q148K Mutation：E138K,Q148K Mutation：E138K,Q148K Mutation：E138K,Q148K Mutation：E138K,Q148K Mutation：E138K,Q148K Mutation：E138K,Q148K | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8FNM Structure of G140A/Q148K HIV-1 intasome with Dolutegravir bound Deposited 2022-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: 12-meric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：G140A,Q148K Mutation：G140A,Q148K Mutation：G140A,Q148K Mutation：G140A,Q148K Mutation：G140A,Q148K Mutation：G140A,Q148K Mutation：G140A,Q148K Mutation：G140A,Q148K | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8FNN Structure of E138K/G140A/Q148K HIV-1 intasome with Dolutegravir bound Deposited 2022-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8FNO Structure of E138K/G140A/Q148R HIV-1 intasome with Dolutegravir bound Deposited 2022-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: 12-meric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：E138K,G140A,Q148R Mutation：E138K,G140A,Q148R Mutation：E138K,G140A,Q148R Mutation：E138K,G140A,Q148R Mutation：E138K,G140A,Q148R Mutation：E138K,G140A,Q148R Mutation：E138K,G140A,Q148R Mutation：E138K,G140A,Q148R | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.46 Å |
| 8FNP Structure of E138K/G140S/Q148H HIV-1 intasome with Dolutegravir bound Deposited 2022-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：E138K,G140S,Q148H Mutation：E138K,G140S,Q148H Mutation：E138K,G140S,Q148H Mutation：E138K,G140S,Q148H Mutation：E138K,G140S,Q148H Mutation：E138K,G140S,Q148H Mutation：E138K,G140S,Q148H Mutation：E138K,G140S,Q148H | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å |
| 8FNQ Structure of E138K/G140A/Q148K HIV-1 intasome with 4d bound Deposited 2022-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
|
Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K Mutation：E138K,G140A,Q148K | OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8T5B HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor EKC-110 Deposited 2023-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1204–1358（155 aa）
Chain B
1204–1358（155 aa）
Chain C
1368–1424（57 aa）
Chain D
1368–1424（57 aa）
|
Not recorded | QD6 (2S)-tert-butoxy{4-(4-chlorophenyl)-2,6-dimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；10% (wt/vol) PEG 8,000, 20% ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, and 0.1 M imidazole-MES (pH 6.5)
|
Resolution 2.08 Å R-free 0.265 |
| 8USY HIV-1 Integrase F185H N222K Complexed with Allosteric Inhibitor BI-D Deposited 2023-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1149–1435（287 aa）
Chain B
1149–1435（287 aa）
|
Mutation：Y15A, F185H, N222K Mutation：Y15A, F185H, N222K | LF0 (2S)-tert-butoxy[4-(3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；294.15 K；30% 2-methyl-2,4--pentanediol (MPD), 0.1M sodium citrate pH 5.6
|
Resolution 4.40 Å R-free 0.339 |
| 8V0Z HIV-1 Integrase F185H W131C Complexed with Allosteric Inhibitor BI-D Deposited 2023-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1149–1435（287 aa）
Chain B
1149–1435（287 aa）
|
Mutation：Y15A, F185H, W131C Mutation：Y15A, F185H, W131C | LF0 (2S)-tert-butoxy[4-(3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；294.15 K；30% 2-methyl-2,4--pentanediol (MPD), 0.1M sodium citrate pH 5.6
|
Resolution 4.56 Å R-free 0.334 |
| 8V23 Crystal structure of HIV-1 capsid N-terminal domain in the presence of Lenacapavir Deposited 2023-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
133–278（146 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；0.17 M Sodium acetate trihydrate, 0.085 M Sodium cacodylate trihydrate pH 6.5, 25.5% w/v Polyethylene glycol 8,000, 15% v/v Glycerol
|
Resolution 2.00 Å R-free 0.286 |
| 8V9C HIV-1 Integrase F185H Complexed with Allosteric Inhibitor GSK1264 Deposited 2023-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1149–1435（287 aa）
Chain B
1149–1435（287 aa）
|
Mutation：Y15A, F185H Mutation：Y15A, F185H | 2SQ (2S)-tert-butoxy[4-(8-fluoro-5-methyl-3,4-dihydro-2H-chromen-6-yl)-2-methyl-1-oxo-1,2-dihydroisoquinolin-3-yl]ethanoic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；294.15 K；30% 2-methyl-2,4 pentanediol (MPD), 0.1 M sodium citrate pH 5.6 - 6.5
|
Resolution 4.40 Å R-free 0.341 |
| 8V9C HIV-1 Integrase F185H Complexed with Allosteric Inhibitor GSK1264 Deposited 2023-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1149–1435（287 aa）
Chain B
1149–1435（287 aa）
|
Mutation：Y15A, F185H Mutation：Y15A, F185H | 2SQ (2S)-tert-butoxy[4-(8-fluoro-5-methyl-3,4-dihydro-2H-chromen-6-yl)-2-methyl-1-oxo-1,2-dihydroisoquinolin-3-yl]ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；294.15 K；30% 2-methyl-2,4 pentanediol (MPD), 0.1 M sodium citrate pH 5.6 - 6.5
|
Resolution 4.40 Å R-free 0.341 |
| 8VC0 HIV-1 CA crosslinked pentamer in complex with GS-CA1 Deposited 2023-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric |
Chain A
133–363（231 aa）
Chain B
133–363（231 aa）
Chain C
133–363（231 aa）
Chain D
133–363（231 aa）
Chain E
133–363（231 aa）
|
Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A | A1AAO N-[(1S)-1-{(3M)-3-{4-chloro-3-[(cyclopropanesulfonyl)amino]-1-(2,2-difluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 8000,
0.1 M HEPES, pH 6.8
|
Resolution 3.46 Å R-free 0.315 |
| 8VC0 HIV-1 CA crosslinked pentamer in complex with GS-CA1 Deposited 2023-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric |
Chain F
133–363（231 aa）
Chain G
133–363（231 aa）
Chain H
133–363（231 aa）
Chain I
133–363（231 aa）
Chain J
133–363（231 aa）
|
Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A | A1AAO N-[(1S)-1-{(3M)-3-{4-chloro-3-[(cyclopropanesulfonyl)amino]-1-(2,2-difluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 8000,
0.1 M HEPES, pH 6.8
|
Resolution 3.46 Å R-free 0.315 |
| 8VXV HIV-1 R18L CA hexamer Deposited 2024-02-06 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
133–363（231 aa）
|
Mutation：R18L | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；50 mM Tris, pH 8, 1 M NaCl, 5 mM 2-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8VXV HIV-1 R18L CA hexamer Deposited 2024-02-06 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
133–363（231 aa）
|
Mutation：R18L | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；50 mM Tris, pH 8, 1 M NaCl, 5 mM 2-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8VXV HIV-1 R18L CA hexamer Deposited 2024-02-06 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
133–363（231 aa）
|
Mutation：R18L | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；50 mM Tris, pH 8, 1 M NaCl, 5 mM 2-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8VXW HIV-1 R18L CA pentamer from capsid-like particles assembled in 1 M NaCl Deposited 2024-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric |
Chain A
133–363（231 aa）
Chain B
133–363（231 aa）
Chain C
133–363（231 aa）
Chain D
133–363（231 aa）
Chain E
133–363（231 aa）
|
Mutation：R18L Mutation：R18L Mutation：R18L Mutation：R18L Mutation：R18L | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；50 mM Tris, pH 8, 1 M NaCl, 5 mM 2-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8X1Z HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y:DNA:E-CFCP-TP ternary complex Deposited 2023-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C162S, C280S | GOL GLYCEROL × 2 MG MAGNESIUM ION × 1 XTE E-CFCP-triphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol
|
Resolution 2.62 Å R-free 0.223 |
| 8X1Z HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y:DNA:E-CFCP-TP ternary complex Deposited 2023-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C162S, C280S | GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 XTE E-CFCP-triphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol
|
Resolution 2.62 Å R-free 0.223 |
| 8X20 HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:E-CFCP-TP ternary complex Deposited 2023-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C162S, C280S | XTE E-CFCP-triphosphate × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol
|
Resolution 2.70 Å R-free 0.231 |
| 8X20 HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:E-CFCP-TP ternary complex Deposited 2023-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C162S, C280S | XTE E-CFCP-triphosphate × 1 GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol
|
Resolution 2.70 Å R-free 0.231 |
| 8X21 HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:ETV-TP ternary complex Deposited 2023-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C162S, C280S | ET9 [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol
|
Resolution 2.33 Å R-free 0.218 |
| 8X21 HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:ETV-TP ternary complex Deposited 2023-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C162S, C280S | ET9 [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol
|
Resolution 2.33 Å R-free 0.218 |
| 8X22 HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:dGTP ternary complex Deposited 2023-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
588–1015（428 aa）
|
Mutation：C162S, C280S | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol
|
Resolution 2.31 Å R-free 0.219 |
| 8X22 HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:dGTP ternary complex Deposited 2023-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain D
588–1015（428 aa）
|
Mutation：C162S, C280S | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol
|
Resolution 2.31 Å R-free 0.219 |
| 8ZH4 HIV-1 integrase core domain in complex with compound 5 Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：F185H Non-standard monomer：Yes (specific site not provided by mmCIF) | PG4 TETRAETHYLENE GLYCOL × 2 A1L1V (2~{S})-2-(4',5-dimethylspiro[1,2-dihydroindene-3,1'-cyclohexane]-4-yl)-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M sodium cacodylate, 0.2M ammonium sulfate, 7% (w/v) PEG 8000, 5mM DTT, soaking the crystal with 1mM compound 5
|
Resolution 1.82 Å R-free 0.220 |
| 8ZHA HIV-1 integrase core domain in complex with compound 15 Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1197–1359（163 aa）
|
Mutation：F185H Non-standard monomer：Yes (specific site not provided by mmCIF) | PG4 TETRAETHYLENE GLYCOL × 2 A1L1W (2~{S})-2-[7-(cycloheptylcarbamoyl)-4',5-dimethyl-spiro[1,2-dihydroindene-3,1'-cyclohexane]-4-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid × 2 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M sodium cacodylate, 0.2M ammonium sulfate, 7% (w/v) PEG 8000, 5mM DTT, soaking the crystal with 1mM compound 15
|
Resolution 1.95 Å R-free 0.211 |
| 9BW9 Tetrameric Complex of full-length HIV-1 integrase protein bound to the integrase binding domain of LEDGF/p75 Deposited 2024-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C
|
Resolution 4.10 Å |
| 9C29 Hexadecamer of NL4-3 WT HIV-1 intasome Deposited 2024-05-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 16 PDB declaration: 20-meric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain E
1148–1435（288 aa）
Chain F
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
Chain K
1148–1435（288 aa）
Chain L
1148–1435（288 aa）
Chain M
1148–1435（288 aa）
Chain N
1148–1435（288 aa）
Chain O
1148–1435（288 aa）
Chain P
1148–1435（288 aa）
|
Not recorded | MG MAGNESIUM ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE；Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C
|
Resolution 8.00 Å |
| 9C9M HIV-1 intasome core bound with DTG Deposited 2024-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: 12-meric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1332–1435（104 aa）
Chain I
1148–1435（288 aa）
Chain K
1148–1435（288 aa）
Chain L
1148–1435（288 aa）
Chain M
1332–1435（104 aa）
|
Not recorded | MG MAGNESIUM ION × 4 ZN ZINC ION × 2 DLU (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.01 Å |
| 9EK1 HIV-1 mature WT matrix protein p17 lattice Deposited 2024-11-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 39 PDB declaration: 39-meric |
Chain A
2–116（115 aa）
Chain B
2–116（115 aa）
Chain C
2–116（115 aa）
Chain D
2–116（115 aa）
Chain E
2–116（115 aa）
Chain F
2–116（115 aa）
Chain G
2–116（115 aa）
Chain H
2–116（115 aa）
Chain I
2–116（115 aa）
Chain J
2–116（115 aa）
Chain K
2–116（115 aa）
Chain L
2–116（115 aa）
Chain M
2–116（115 aa）
Chain N
2–116（115 aa）
Chain O
2–116（115 aa）
Chain P
2–116（115 aa）
Chain Q
2–116（115 aa）
Chain R
2–116（115 aa）
Chain S
2–116（115 aa）
Chain T
2–116（115 aa）
Chain U
2–116（115 aa）
Chain V
2–116（115 aa）
Chain W
2–116（115 aa）
Chain X
2–116（115 aa）
Chain Y
2–116（115 aa）
Chain Z
2–116（115 aa）
Chain a
2–116（115 aa）
Chain b
2–116（115 aa）
Chain c
2–116（115 aa）
Chain d
2–116（115 aa）
Chain e
2–116（115 aa）
Chain f
2–116（115 aa）
Chain g
2–116（115 aa）
Chain h
2–116（115 aa）
Chain i
2–116（115 aa）
Chain j
2–116（115 aa）
Chain k
2–116（115 aa）
Chain l
2–116（115 aa）
Chain m
2–116（115 aa）
|
Not recorded | MYR MYRISTIC ACID × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.30 Å |
| 9EK2 HIV-1 immature L20K/E73K/A82T matrix protein p17 lattice Deposited 2024-11-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 39 PDB declaration: 39-meric |
Chain A
2–116（115 aa）
Chain B
2–116（115 aa）
Chain C
2–116（115 aa）
Chain D
2–116（115 aa）
Chain E
2–116（115 aa）
Chain F
2–116（115 aa）
Chain G
2–116（115 aa）
Chain H
2–116（115 aa）
Chain I
2–116（115 aa）
Chain J
2–116（115 aa）
Chain K
2–116（115 aa）
Chain L
2–116（115 aa）
Chain M
2–116（115 aa）
Chain N
2–116（115 aa）
Chain O
2–116（115 aa）
Chain P
2–116（115 aa）
Chain Q
2–116（115 aa）
Chain R
2–116（115 aa）
Chain S
2–116（115 aa）
Chain T
2–116（115 aa）
Chain U
2–116（115 aa）
Chain V
2–116（115 aa）
Chain W
2–116（115 aa）
Chain X
2–116（115 aa）
Chain Y
2–116（115 aa）
Chain Z
2–116（115 aa）
Chain a
2–116（115 aa）
Chain b
2–116（115 aa）
Chain c
2–116（115 aa）
Chain d
2–116（115 aa）
Chain e
2–116（115 aa）
Chain f
2–116（115 aa）
Chain g
2–116（115 aa）
Chain h
2–116（115 aa）
Chain i
2–116（115 aa）
Chain j
2–116（115 aa）
Chain k
2–116（115 aa）
Chain l
2–116（115 aa）
Chain m
2–116（115 aa）
|
Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T Mutation：L20K,E73K,A82T | MYR MYRISTIC ACID × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.30 Å |
| 9EK3 HIV-1 immature WT matrix protein p17 lattice Deposited 2024-11-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 39 PDB declaration: 39-meric |
Chain A
2–116（115 aa）
Chain B
2–116（115 aa）
Chain C
2–116（115 aa）
Chain D
2–116（115 aa）
Chain E
2–116（115 aa）
Chain F
2–116（115 aa）
Chain G
2–116（115 aa）
Chain H
2–116（115 aa）
Chain I
2–116（115 aa）
Chain J
2–116（115 aa）
Chain K
2–116（115 aa）
Chain L
2–116（115 aa）
Chain M
2–116（115 aa）
Chain N
2–116（115 aa）
Chain O
2–116（115 aa）
Chain P
2–116（115 aa）
Chain Q
2–116（115 aa）
Chain R
2–116（115 aa）
Chain S
2–116（115 aa）
Chain T
2–116（115 aa）
Chain U
2–116（115 aa）
Chain V
2–116（115 aa）
Chain W
2–116（115 aa）
Chain X
2–116（115 aa）
Chain Y
2–116（115 aa）
Chain Z
2–116（115 aa）
Chain a
2–116（115 aa）
Chain b
2–116（115 aa）
Chain c
2–116（115 aa）
Chain d
2–116（115 aa）
Chain e
2–116（115 aa）
Chain f
2–116（115 aa）
Chain g
2–116（115 aa）
Chain h
2–116（115 aa）
Chain i
2–116（115 aa）
Chain j
2–116（115 aa）
Chain k
2–116（115 aa）
Chain l
2–116（115 aa）
Chain m
2–116（115 aa）
|
Not recorded | MYR MYRISTIC ACID × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.00 Å |
| 9N0V Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, KFA-027 Deposited 2025-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
133–352（220 aa）
Chain B
133–352（220 aa）
|
Not recorded | A1BUL N-[(1S)-1-{(3M)-3-[4-chloro-3-(methanesulfonamido)-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl]-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-phenylethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM NaI, 100 mM Sodium cacodylate pH 6.5, 6% glycerol, 9% PEG 3350
|
Resolution 2.98 Å R-free 0.309 |
| 9N0V Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, KFA-027 Deposited 2025-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain C
133–352（220 aa）
Chain D
133–352（220 aa）
|
Not recorded | A1BUL N-[(1S)-1-{(3M)-3-[4-chloro-3-(methanesulfonamido)-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl]-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-phenylethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM NaI, 100 mM Sodium cacodylate pH 6.5, 6% glycerol, 9% PEG 3350
|
Resolution 2.98 Å R-free 0.309 |
| 9NLP HIV-1 Reverse Transcriptase with New Non-Nucleoside Reverse Transcriptase Inhibitor 12126065 Deposited 2025-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
588–1147（560 aa）
Chain B
588–1027（440 aa）
|
Not recorded | A1BYY 4-({5-amino-1-[6-(2-cyanoethyl)naphthalene-1-sulfonyl]-1H-1,2,4-triazol-3-yl}amino)-2-chlorobenzonitrile × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；50mM Tris-HCl pH=8, 60mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；The cryo-EM grids used for single particle collection were Quantifoil R 2/1 300 gold mesh grids with carbon coating. The grids were glow-discharged for 25 s at 25 mA with the chamber pressure set at 0.3 mbar (PELCO easiGlow; Ted Pella). The grids were prepared using the Leica GP2 plunge freezer with its chamber set to 10oC and 95% humidity. Samples of purified HIV-1 RT were diluted to 1mg/mL and 2 molar equivalents of the appropriate compound 12126065 were incubated on a 4oC rotator overnight to combine. A total of 4uL of HIV-1 RT and compound were applied to the backside of the Quantifoil grid and blotted for 4 seconds on the carbon side before plunge frozen in ethane at -181oC.
|
Resolution 3.53 Å |
| 9ON8 Immature HIV-1 CACTD-SP1 lattice with Maturation inhibitor PF-46396 (R) and Inositol hexakisphosphate (IP6) Deposited 2025-05-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain G
278–377（100 aa）
Fragment：residues 278-377
Chain H
278–377（100 aa）
Fragment：residues 278-377
Chain I
278–377（100 aa）
Fragment：residues 278-377
Chain J
278–377（100 aa）
Fragment：residues 278-377
Chain K
278–377（100 aa）
Fragment：residues 278-377
Chain L
278–377（100 aa）
Fragment：residues 278-377
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 A1CCY 1-{(2R)-2-(4-tert-butylphenyl)-2-[(2,3-dihydro-1H-inden-2-yl)amino]ethyl}-3-(trifluoromethyl)pyridin-2(1H)-one × 1 |
SOLID-STATE NMR
NMR measurement conditions
pH 8；277 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；310 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；306 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；288 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；263 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, deuterated protein buffer | deuterated protein buffer
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (R), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
|
Resolution not provided |
| 9ON9 Immature HIV-1 CACTD-SP1 lattice with Maturation inhibitor PF-46396 (R) and Inositol hexakisphosphate (IP6) Deposited 2025-05-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain G
278–377（100 aa）
Fragment：residues 278-377
Chain H
278–377（100 aa）
Fragment：residues 278-377
Chain I
278–377（100 aa）
Fragment：residues 278-377
Chain J
278–377（100 aa）
Fragment：residues 278-377
Chain K
278–377（100 aa）
Fragment：residues 278-377
Chain L
278–377（100 aa）
Fragment：residues 278-377
|
Not recorded | A1CCY 1-{(2R)-2-(4-tert-butylphenyl)-2-[(2,3-dihydro-1H-inden-2-yl)amino]ethyl}-3-(trifluoromethyl)pyridin-2(1H)-one × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 |
SOLID-STATE NMR
NMR measurement conditions
pH 8；277 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；310 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；306 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；288 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；263 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, deuterated protein buffer | deuterated protein buffer
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (R), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
|
Resolution not provided |
| 9ONA Immature HIV-1 CACTD-SP1 lattice with Maturation inhibitor PF-46396 (S) and Inositol hexakisphosphate (IP6) Deposited 2025-05-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain G
278–377（100 aa）
Fragment：residues 278-377
Chain H
278–377（100 aa）
Fragment：residues 278-377
Chain I
278–377（100 aa）
Fragment：residues 278-377
Chain J
278–377（100 aa）
Fragment：residues 278-377
Chain K
278–377（100 aa）
Fragment：residues 278-377
Chain L
278–377（100 aa）
Fragment：residues 278-377
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 A1CCZ 1-{(2S)-2-(4-tert-butylphenyl)-2-[(2,3-dihydro-1H-inden-2-yl)amino]ethyl}-3-(trifluoromethyl)pyridin-2(1H)-one × 1 |
SOLID-STATE NMR
NMR measurement conditions
pH 8；277 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；310 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；306 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；288 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；263 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
NMR sample composition
400 uM [U-13C; U-15N; U-2H] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (S), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
|
Resolution not provided |
| 9ONB Immature HIV-1 CACTD-SP1 lattice with Maturation inhibitor PF-46396 (S) and Inositol hexakisphosphate (IP6) Deposited 2025-05-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain G
278–377（100 aa）
Fragment：residues 278-377
Chain H
278–377（100 aa）
Fragment：residues 278-377
Chain I
278–377（100 aa）
Fragment：residues 278-377
Chain J
278–377（100 aa）
Fragment：residues 278-377
Chain K
278–377（100 aa）
Fragment：residues 278-377
Chain L
278–377（100 aa）
Fragment：residues 278-377
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 A1CCZ 1-{(2S)-2-(4-tert-butylphenyl)-2-[(2,3-dihydro-1H-inden-2-yl)amino]ethyl}-3-(trifluoromethyl)pyridin-2(1H)-one × 1 |
SOLID-STATE NMR
NMR measurement conditions
pH 8；277 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；310 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；306 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；306 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR measurement conditions
pH 8；263 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 CACTD-SP1/PF-46396(racem)/IP6, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
NMR sample composition
400 uM [U-13C; U-15N; U-2H] HIV-1 CACTD-SP1/PF-46396(racem)/IP6, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
NMR sample composition
400 uM [U-100% 13C; U-100% 15N] HIV-1 CACTD-SP1/PF-46396(racem)/IP6, 360 uM PF-46396 (S), 400 uM INOSITOL HEXAKISPHOSPHATE, protein buffer | protein buffer
|
Resolution not provided |
| 9PYX Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor J02-30 Deposited 2025-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | A1CM5 (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-1-(3,5-difluorophenyl)-4-[(2-ethylbutyl){4-[(1R)-1-hydroxyethyl]benzene-1-sulfonyl}amino]-3-hydroxybutan-2-yl}carbamate × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% w/v ammonium sulfate, 0.1 M Bis-Tris-methane-HCl, pH 5.5
|
Resolution 1.73 Å R-free 0.247 |
| 9PZ1 Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor LR4-43 Deposited 2025-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 1 A1CM6 (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-1-(3,5-difluorophenyl)-4-[(2-ethylbutyl){4-[(1S)-1-hydroxyethyl]benzene-1-sulfonyl}amino]-3-hydroxybutan-2-yl}carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% w/v ammonium sulfate, 0.1 M Bis-Tris-methane-HCl, pH 5.5
|
Resolution 1.80 Å R-free 0.253 |
| 9Q0T Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor NR05-01 Deposited 2025-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | SO4 SULFATE ION × 3 A1CNI (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-{[(1S)-1-hydroxy-2,3-dihydro-1H-indene-5-sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% w/v ammonium sulfate, 0.1 M Bis-Tris-methane-HCl, pH 5.5
|
Resolution 1.87 Å R-free 0.234 |
| 9Q13 Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor NR05-04 Deposited 2025-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | A1CNJ (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-{[(1R)-1-hydroxy-2,3-dihydro-1H-indene-5-sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% w/v ammonium sulfate, 0.1 M Bis-Tris-methane-HCl, pH 5.5
|
Resolution 1.72 Å R-free 0.237 |
| 9Q1C Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor LR4-46 Deposited 2025-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | A1CNK (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-[{4-[(1R)-1-hydroxyethyl]benzene-1-sulfonyl}(2-methylpropyl)amino]butan-2-yl}carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% w/v ammonium sulfate, 0.1 M Bis-Tris-methane-HCl, pH 5.5
|
Resolution 1.94 Å R-free 0.252 |
| 9Q1P Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor NR05-03 Deposited 2025-08-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | A1CNO (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-4-{(2-ethylbutyl)[(1S)-1-hydroxy-2,3-dihydro-1H-indene-5-sulfonyl]amino}-3-hydroxybutan-2-yl]carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% w/v ammonium sulfate, 0.1 M Bis-Tris-methane-HCl, pH 5.5
|
Resolution 1.87 Å R-free 0.255 |
| 9Q3P Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor LR4-45 Deposited 2025-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | A1CNY (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-({4-[(1S)-1-hydroxyethyl]benzene-1-sulfonyl}[(2S)-2-methylbutyl]amino)butan-2-yl]carbamate × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5
|
Resolution 1.90 Å R-free 0.242 |
| 9Q3T Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor NR03-92 Deposited 2025-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | SO4 SULFATE ION × 1 A1CNZ (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-3-hydroxy-4-{[(1R)-1-hydroxy-2,3-dihydro-1H-indene-5-sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5
|
Resolution 1.87 Å R-free 0.246 |
| 9Q50 AK01 integrase inhibitor bound to Wild-type HIV-1 intasome Deposited 2025-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 A1COF 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-5-(hydroxymethyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE；Cryo-EM grids were prepared by freezing using a Vitrobot plunge freezer (Thermo Fisher Scientific) at 20C with 100% humidity
|
Resolution 2.33 Å |
| 9Q57 XZ440 integrase inhibitor bound to Wild-type HIV-1 intasome Deposited 2025-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 R7K ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-5-(hydroxymethyl)-1,4-bis(oxidanyl)-2-oxidanylidene-1,8-naphthyridine-3-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE；Cryo-EM grids were prepared by freezing using a Vitrobot plunge freezer (Thermo Fisher Scientific) at 20C with 100% humidity
|
Resolution 2.28 Å |
| 9Q5D Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor J02-37 Deposited 2025-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
489–587（99 aa）
Chain B
489–587（99 aa）
|
Not recorded | A1COE (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-({4-[(1R)-1-hydroxyethyl]benzene-1-sulfonyl}[(2S)-2-methylbutyl]amino)butan-2-yl]carbamate × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23-24% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5
|
Resolution 1.94 Å R-free 0.243 |
| 9RMX CryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm) Deposited 2025-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 44 PDB declaration: 44-meric |
Chain A
1148–1435（288 aa）
Chain B
1148–1435（288 aa）
Chain C
1148–1435（288 aa）
Chain D
1148–1435（288 aa）
Chain E
1148–1435（288 aa）
Chain F
1148–1435（288 aa）
Chain G
1148–1435（288 aa）
Chain H
1148–1435（288 aa）
Chain I
1148–1435（288 aa）
Chain J
1148–1435（288 aa）
Chain K
1148–1435（288 aa）
Chain L
1148–1435（288 aa）
|
Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N Mutation：D64N, D116N | ZN ZINC ION × 12 IHP INOSITOL HEXAKISPHOSPHATE × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.63 Å |
163 other PDB entries and 211 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | POL_HV1N5 |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–231； UniProt 133–363 |
