Integrase
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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 50–209 | Mutation：C56S, F139D, F185H | O20 (2S)-tert-butoxy[(5M)-5-{2-[(2-chloro-6-methylphenyl)methyl]-1,2,3,4-tetrahydroisoquinolin-6-yl}-4-(4,4-dimethylpiperidin-1-yl)-2-methylpyridin-3-yl]acetic acid × 2 SO4 SULFATE ION × 6 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.2-0.18M Ammonium Sulfate, 100mM Na acetate | Resolution 1.89 Å R-free 0.224 |
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 7UOQ | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1BIZ HIV-1 INTEGRASE CORE DOMAIN Deposited 1998-06-21 | Different construct Different mutation/modification 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, RESIDUES 54 - 212
Chain B
762–927（166 aa）
Fragment：CORE DOMAIN, RESIDUES 54 - 212
|
Mutation：C56S, F185K Mutation：C56S, F185K | CAC CACODYLATE ION × 4 |
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 0.253 |
| 1HYV HIV INTEGRASE CORE DOMAIN COMPLEXED WITH TETRAPHENYL ARSONIUM Deposited 2001-01-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC CORE DOMAIN (RESIDUES 50-212)
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 TTA TETRAPHENYL-ARSONIUM × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG8000, NH4SO4, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.263 |
| 1HYZ HIV INTEGRASE CORE DOMAIN COMPLEXED WITH A DERIVATIVE OF TETRAPHENYL ARSONIUM. Deposited 2001-01-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC CORE DOMAIN (RESIDUES 50-212)
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 TTO (3,4-DIHYDROXY-PHENYL)-TRIPHENYL-ARSONIUM × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG8000, NH4SO4, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.291 |
| 1QS4 Core domain of HIV-1 integrase complexed with Mg++ and 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone Deposited 1999-06-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
771–924（154 aa）
Fragment：Catalytic core domain
Chain B
771–924（154 aa）
Fragment：Catalytic core domain
|
Mutation：F185K, W131E Mutation：F185K, W131E | MG MAGNESIUM ION × 2 100 1-(5-CHLOROINDOL-3-YL)-3-HYDROXY-3-(2H-TETRAZOL-5-YL)-PROPENONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；30% PEG 4000, 100 MM HEPES, 5 MM MGCL2, 5 MM DTT, 1% GLYCEROL, pH 7.00
|
Resolution 2.10 Å R-free 0.255 |
| 1QS4 Core domain of HIV-1 integrase complexed with Mg++ and 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone Deposited 1999-06-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
771–924（154 aa）
Fragment：Catalytic core domain
|
Mutation：F185K, W131E | MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；30% PEG 4000, 100 MM HEPES, 5 MM MGCL2, 5 MM DTT, 1% GLYCEROL, pH 7.00
|
Resolution 2.10 Å R-free 0.255 |
| 3LPT HIV integrase Deposited 2010-02-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：HIV integrase core domain
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | 723 (6-chloro-2-oxo-4-phenyl-1,2-dihydroquinolin-3-yl)acetic acid × 2 PEG DI(HYDROXYETHYL)ETHER × 8 P03 2-[3-[3-(2-hydroxyethoxy)propoxy]propoxy]ethanol × 2 SO4 SULFATE ION × 6 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；277 K；10% (w/v) PEG 8000, 0.1M Na cacodylate pH 6.5, 0.1M (NH4)2SO4, 5mM DTT, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.00 Å R-free 0.272 |
| 3LPU HIV integrase Deposited 2010-02-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：HIV integrase core domain
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | 976 (2S)-2-(6-chloro-2-methyl-4-phenylquinolin-3-yl)pentanoic acid × 2 P03 2-[3-[3-(2-hydroxyethoxy)propoxy]propoxy]ethanol × 2 PEG DI(HYDROXYETHYL)ETHER × 4 SO4 SULFATE ION × 6 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10% (w/v) PEG 8000, 0.1M Na cacodylate pH 6.5, 0.1M (NH4)2SO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.221 |
| 3NF6 Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design Deposited 2010-06-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：catalytic domain, residues 50-212
Chain B
50–212（163 aa）
Fragment：catalytic domain, residues 50-212
|
Mutation：F185H, C56S, F139D Mutation：F185H, C56S, F139D | SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 2 ACY ACETIC ACID × 2 IMV 5-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；1.7M ammonium sulfate, 0.1M sodium acetate pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.208 |
| 3NF7 Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design Deposited 2010-06-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：catalytic domain, UNP residues 50-212
Chain B
50–212（163 aa）
Fragment：catalytic domain, UNP residues 50-212
|
Mutation：F185H, C56S, F139D Mutation：F185H, C56S, F139D | SO4 SULFATE ION × 10 ACY ACETIC ACID × 7 EDO 1,2-ETHANEDIOL × 2 CIW 5-[(5-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；1.7M ammonium sulfate, 0.1M sodium acetate pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.207 |
| 3NF8 Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design Deposited 2010-06-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：catalytic domain, residues 50-212
Chain B
50–212（163 aa）
Fragment：catalytic domain, residues 50-212
|
Mutation：F185H, C56S, F139D Mutation：F185H, C56S, F139D | SO4 SULFATE ION × 6 CDQ 6-[(5-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 6 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；1.7M ammonium sulfate, 0.1M sodium acetate pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.198 |
| 3NF9 Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design Deposited 2010-06-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：catalytic domain, residues 50-212
Chain B
50–212（163 aa）
Fragment：catalytic domain, residues 50-212
|
Mutation：F185H, C56S, F139D Mutation：F185H, C56S, F139D | SO4 SULFATE ION × 11 CD9 5-[(6-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid × 2 EDO 1,2-ETHANEDIOL × 2 ACY ACETIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；1.7M ammonium sulfate, 0.1M sodium acetate pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.208 |
| 3NFA Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design Deposited 2010-06-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：catalytic domain, residues 50-212
Chain B
50–212（163 aa）
Fragment：catalytic domain, residues 50-212
|
Mutation：F185H, C56S, F139D Mutation：F185H, C56S, F139D | SO4 SULFATE ION × 8 CBJ 6-[(5-bromo-2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 4 ACY ACETIC ACID × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；1.7M ammonium sulfate, 0.1M sodium acetate pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.204 |
| 3ZCM Small molecule inhibitors of the LEDGF site of HIV integrase identified by fragment screening and structure based design. Deposited 2012-11-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 GOL GLYCEROL × 2 PX3 5-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-prop-2-enyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.204 |
| 3ZSO Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design Deposited 2011-06-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACY ACETIC ACID × 4 NA SODIUM ION × 2 O2N 5-{[(2-{[bis(4-methoxyphenyl)methyl]carbamoyl}benzyl)(prop-2-en-1-yl)amino]methyl}-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；1.7 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
|
Resolution 1.75 Å R-free 0.209 |
| 3ZSQ Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-06-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACY ACETIC ACID × 3 O4N 5-[[[2-[[(1S)-1-(4-METHOXYPHENYL)BUTYL]CARBAMOYL]PHENYL]METHYL-PROP-2-ENYL-AMINO]METHYL]-1,3-BENZODIOXOLE-4-CARBOXYLIC ACID × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.200 |
| 3ZSR Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-06-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 O3N (2S)-2-(2-carboxyethyl)-6-{[{2-[(cyclohexylmethyl)carbamoyl]benzyl}(prop-2-en-1-yl)amino]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40MM TRIS PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0M AMMONIUM SULFATE, 100MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5
|
Resolution 1.70 Å R-free 0.193 |
| 3ZSV Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACY ACETIC ACID × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2 ZSV (R)-[(2S)-5-carboxy-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl-[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl]-prop-2-enyl-azanium × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.75 Å R-free 0.198 |
| 3ZSW Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | THR THREONINE × 2 SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 ACY ACETIC ACID × 1 GOL GLYCEROL × 2 ZSW (R)-[2-[[(2R)-butan-2-yl]carbamoyl]phenyl]methyl-[[(2S)-5-carboxy-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl]-prop-2-enyl-azanium × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.206 |
| 3ZSX Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2 N44 5-({[2-(benzylcarbamoyl)benzyl](prop-2-en-1-yl)amino}methyl)-1,3-benzodioxole-4-carboxylate × 2 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.228 |
| 3ZSY Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 2 OM3 (R)-(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-(CYCLOHEXYLMETHYLCARBAMOYL)PHENYL]METHYL]-METHYL-AZANIUM × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.20 Å R-free 0.222 |
| 3ZSZ Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 5 OM2 (R)-[2-[[(2S)-BUTAN-2-YL]CARBAMOYL]PHENYL]METHYL-[(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL]-METHYL-AZANIUM × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.00 Å R-free 0.222 |
| 3ZT0 Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ZT0 (4-CARBOXY-1,3-BENZODIOXOL-5-YL)-N-{2-[(4-METHOXYBENZYL)CARBAMOYL]BENZYL}-N-METHYLMETHANAMINIUM × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.240 |
| 3ZT1 Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 7 EDO 1,2-ETHANEDIOL × 3 OM1 (4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-[(4-METHOXYPHENYL)METHYLCARBAMOYL]PHENYL]METHYL]AZANIUM × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 4 0MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.75 Å R-free 0.199 |
| 3ZT2 Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 4 ZT2 5-[(E)-(2-OXO-2,3-DIHYDRO-1H-INDEN-1-YLIDENE)METHYL]-1,3-BENZODIOXOLE-4-CARBOXYLIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40MM TRIS PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0M AMMONIUM SULFATE, 100MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5
|
Resolution 1.70 Å R-free 0.216 |
| 3ZT3 Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACY ACETIC ACID × 7 EDO 1,2-ETHANEDIOL × 1 ZT4 5-{(E)-[(2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YLIDENE]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40MM TRIS PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0M AMMONIUM SULFATE, 100MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5
|
Resolution 1.95 Å R-free 0.216 |
| 3ZT4 Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design Deposited 2011-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
Chain B
56–212（157 aa）
Fragment：CORE CATALYTIC DOMAIN, RESIDUES 56-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACY ACETIC ACID × 2 EDO 1,2-ETHANEDIOL × 1 ZT2 5-[(E)-(2-OXO-2,3-DIHYDRO-1H-INDEN-1-YLIDENE)METHYL]-1,3-BENZODIOXOLE-4-CARBOXYLIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.20 Å R-free 0.229 |
| 4CE9 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACY ACETIC ACID × 2 GOL GLYCEROL × 2 O3N (2S)-2-(2-carboxyethyl)-6-{[{2-[(cyclohexylmethyl)carbamoyl]benzyl}(prop-2-en-1-yl)amino]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.10 Å R-free 0.213 |
| 4CEA Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 ACY ACETIC ACID × 1 GOL GLYCEROL × 2 ZSW (R)-[2-[[(2R)-butan-2-yl]carbamoyl]phenyl]methyl-[[(2S)-5-carboxy-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl]-prop-2-enyl-azanium × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.206 |
| 4CEB Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACY ACETIC ACID × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2 ZSV (R)-[(2S)-5-carboxy-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl-[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl]-prop-2-enyl-azanium × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.75 Å R-free 0.198 |
| 4CEC Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 2SS (2S)-6-[[[2-(cyclobutylmethylcarbamoyl)phenyl]methyl-prop-2-enyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.75 Å R-free 0.195 |
| 4CED Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 9NS (2S)-6-[[[2-(furan-2-ylmethylcarbamoyl)phenyl]methyl-prop-2-enyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.75 Å R-free 0.194 |
| 4CEE Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-512
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-512
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 B0T (2S)-6-[[[2-[[(2S)-butan-2-yl]carbamoyl]phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.201 |
| 4CEF Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-512
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-512
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 D0T (2S)-2-(3-hydroxy-3-oxopropyl)-6-[[methyl-[[2-[(phenylmethyl)carbamoyl]phenyl]methyl]amino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.200 |
| 4CEO Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 1 ACT ACETATE ION × 2 G0T (2S)-2-(3-hydroxy-3-oxopropyl)-6-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-methyl-amino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.90 Å R-free 0.195 |
| 4CEQ Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 1 CL CHLORIDE ION × 2 QCH (2S)-6-[[[2-(cyclohexylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.198 |
| 4CER Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 VL4 (2S)-6-[[[2-(cyclobutylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.201 |
| 4CES Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 CL CHLORIDE ION × 2 NFW (2S)-6-[[[2-(furan-2-ylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.85 Å R-free 0.197 |
| 4CEZ Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 O3N (2S)-2-(2-carboxyethyl)-6-{[{2-[(cyclohexylmethyl)carbamoyl]benzyl}(prop-2-en-1-yl)amino]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.193 |
| 4CF0 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 O5U (2R)-6-[[(1R,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.85 Å R-free 0.225 |
| 4CF1 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACT ACETATE ION × 3 IY7 (2s)-6-[[(1r,2s)-2-(5-azanylpentanoylamino)-2,3-dihydro-1h-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.209 |
| 4CF2 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 3GM (2s)-6-[[(1r,2s)-2-(4-azanylbutanoylamino)-2,3-dihydro-1h-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.227 |
| 4CF8 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACY ACETIC ACID × 5 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 3 GOL GLYCEROL × 2 V7H (2S)-2-(3-hydroxy-3-oxopropyl)-6-[[[2-[(phenylmethyl)carbamoyl]phenyl]methylamino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.65 Å R-free 0.196 |
| 4CF9 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 EDO 1,2-ETHANEDIOL × 1 5EY (3R)-3-(3-hydroxy-3-oxopropyl)-6-[(E)-[(2R)-2-oxidanyl-2,3-dihydroinden-1-ylidene]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 EE2 (2R)-2-(3-hydroxy-3-oxopropyl)-6-[(E)-[(2S)-2-oxidanyl-2,3-dihydroinden-1-ylidene]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.10 Å R-free 0.199 |
| 4CFA Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 WOP 5-[[methyl-[[(1S)-2-oxidanylidene-1-phenyl-2-[(phenylmethyl)amino]ethyl]carbamoyl]amino]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5
|
Resolution 2.05 Å R-free 0.215 |
| 4CFB Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 5 OM3 (R)-(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-(CYCLOHEXYLMETHYLCARBAMOYL)PHENYL]METHYL]-METHYL-AZANIUM × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.219 |
| 4CFC Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACT ACETATE ION × 2 CL CHLORIDE ION × 2 7NV 5-[[[(1S)-2-(butylamino)-2-oxidanylidene-1-phenyl-ethyl]carbamoyl-methyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.90 Å R-free 0.220 |
| 4CFD Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 4 CL CHLORIDE ION × 2 S8Y 5-[[[(1R)-2-(tert-butylamino)-2-oxidanylidene-1-phenyl-ethyl]carbamoyl-methyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.15 Å R-free 0.237 |
| 4CGD Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACY ACETIC ACID × 2 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 8P3 2-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]benzoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.00 Å R-free 0.232 |
| 4CGF Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 ACT ACETATE ION × 8 EDO 1,2-ETHANEDIOL × 3 UJ6 5-{[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5
|
Resolution 1.70 Å R-free 0.230 |
| 4CGG Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 K5Q (2S)-6-[(E)-[(2E)-2-hydroxyimino-3H-inden-1-ylidene]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.75 Å R-free 0.199 |
| 4CGH Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 7 ACY ACETIC ACID × 2 LOZ 5-[[(1S,2R)-2-(4-azanylbutanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.76 Å R-free 0.203 |
| 4CGI Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 2 NZL 5-[[(1S,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.07 Å R-free 0.211 |
| 4CGJ Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACT ACETATE ION × 2 NZL 5-[[(1S,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.15 Å R-free 0.200 |
| 4CHN Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 5 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 ONZ 2-(1,3-benzodioxol-4-ylcarbonylamino)ethanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.00 Å R-free 0.194 |
| 4CHO Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 3 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 2 U2Z [1-[2-(aminomethyl)phenyl]-5-methyl-pyrazol-3-yl]methanol × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.198 |
| 4CHP Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 4 IMV 5-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.90 Å R-free 0.198 |
| 4CHQ Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 3 ACT ACETATE ION × 2 CWU 5-[[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.203 |
| 4CHY Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACY ACETIC ACID × 4 EDO 1,2-ETHANEDIOL × 1 C5Q 5-(1H-indol-3-ylmethyl)-1,3-benzodioxole-4-carboxylic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.227 |
| 4CHZ Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 4 CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 5 H75 2-(4-bromophenyl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3(2H)-one × 1 LYS LYSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.195 |
| 4CIF Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACT ACETATE ION × 2 CL CHLORIDE ION × 3 JDX 2-methoxy-6-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-methyl-amino]methyl]benzoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.191 |
| 4CIG Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACT ACETATE ION × 8 X0P 2-methoxy-6-[[[3-[(4-methoxyphenyl)methylcarbamoyl]naphthalen-2-yl]methyl-methyl-amino]methyl]benzoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.188 |
| 4CJ3 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 E4F 5-[[(1R,2S)-2-(5-azanylpentanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid × 2 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.212 |
| 4CJ4 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 4 CL CHLORIDE ION × 2 S3G 5-[(2S)-4-methyl-2-[(pyridin-4-ylcarbonylamino)methyl]pentyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.215 |
| 4CJ5 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 2 CL CHLORIDE ION × 2 4VW 5-[(2S)-2-[[(4-aminophenyl)carbonylamino]methyl]-4-methyl-pentyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.201 |
| 4CJE Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 Q31 5-[(2S)-2-[[2-(1H-imidazol-4-yl)ethanoylamino]methyl]-4-methyl-pentyl]-1,3-benzodioxole-4-carboxylic acid × 2 CL CHLORIDE ION × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.90 Å R-free 0.195 |
| 4CJF Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 2 ACT ACETATE ION × 5 RVN 5-[(E)-(2-oxidanylidene-1H-indol-3-ylidene)methyl]-1,3-benzodioxole-4-carboxylic acid × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.90 Å R-free 0.210 |
| 4CJK Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 4 CL CHLORIDE ION × 2 H39 5-[(2S)-4-methyl-2-{[(1H-pyrrol-3-ylacetyl)amino]methyl}pentyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.75 Å R-free 0.193 |
| 4CJL Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES | SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 ACT ACETATE ION × 2 9PA 5-[(2S)-2-{[(5-aminopentanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.77 Å R-free 0.229 |
| 4CJP Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 7 CL CHLORIDE ION × 2 4D2 5-[(2S)-4-methyl-2-[(pyridin-3-ylcarbonylamino)methyl]pentyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 2.00 Å R-free 0.195 |
| 4CJQ Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 7 ACT ACETATE ION × 3 VXO 5-[(2S)-2-[[2-(1H-indol-3-yl)ethanoylamino]methyl]-4-methyl-pentyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.201 |
| 4CJR Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 9 CL CHLORIDE ION × 1 FYM 2-methoxy-6-[[[6-[(4-methoxyphenyl)methylcarbamoyl]-1,3-benzodioxol-5-yl]methyl-methyl-amino]methyl]benzoic acid × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.195 |
| 4CJS Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACT ACETATE ION × 4 CL CHLORIDE ION × 2 L0Y 6-[[[2-(cyclohexylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.80 Å R-free 0.190 |
| 4CJT Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 GOL GLYCEROL × 2 ACT ACETATE ION × 2 HLR 1,2-benzoxazol-3-amine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.71 Å R-free 0.194 |
| 4CJU Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 5 JNS 5-[(Z)-2-phenylethenyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.199 |
| 4CJV Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 4 GOL GLYCEROL × 2 IV2 5-chloranyl-4-methyl-1,3-benzothiazol-2-amine × 2 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.208 |
| 4CJW Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 ACT ACETATE ION × 4 CBJ 6-[(5-bromo-2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.95 Å R-free 0.197 |
| 4CK1 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 2 OM1 (4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-[(4-METHOXYPHENYL)METHYLCARBAMOYL]PHENYL]METHYL]AZANIUM × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.75 Å R-free 0.185 |
| 4CK2 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 6 ACT ACETATE ION × 4 NVU 2-(1,2-benzoxazol-3-yl)ethanoic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.85 Å R-free 0.211 |
| 4CK3 Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-12-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
Chain B
50–212（163 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 50-212
|
Mutation：YES Mutation：YES | SO4 SULFATE ION × 7 ACT ACETATE ION × 4 K1T 5-[(2S)-2-{[(4-aminobutanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.79 Å R-free 0.212 |
| 4OVL Interrogating HIV integrase for compounds that bind- a SAMPL challenge Deposited 2013-11-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Chain B
50–212（163 aa）
|
Mutation：C56S, F139D, F185H Mutation：C56S, F139D, F185H | SO4 SULFATE ION × 6 ACY ACETIC ACID × 7 1TD 3-[(E)-(2-oxidanylidene-1H-indol-3-ylidene)methyl]benzoic acid × 2 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 mM TRIS PH 8.0, 250 mM NACL, 30 mM MGCL2, 5 mM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 mM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
|
Resolution 1.70 Å R-free 0.215 |
| 4Y1C Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase core domain Deposited 2015-02-07 | Different construct Different mutation/modification 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
50–212（163 aa）
Fragment：residues 50-212
Chain B
50–212（163 aa）
Fragment：residues 50-212
|
Mutation：C56S, W131D, F139D, F185H Mutation：C56S, W131D, F139D, F185H | CD CADMIUM ION × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8M AMMONIUM SULFATE, 0.15M SODIUM
REMARK 280 CITRATE, 5MM CADMIUM CHLORIDE, PH 4.6
|
Resolution 2.30 Å R-free 0.295 |
| 5KGW HIV1 catalytic core domain in complex with inhibitor: (2~{S})-2-[3-(3,4-dihydro-2~{H}-chromen-6-yl)-1-methyl-indol-2-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid Deposited 2016-06-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 6 7SK (2S)-tert-butoxy[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-1-methyl-1H-indol-2-yl]acetic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；277 K；8%PEG 8K
.1M Ammonium Sulfate
.1M Na-cacodylate pH 6.5
5mM DTT
|
Resolution 2.34 Å R-free 0.241 |
| 5KGX HIV1 catalytic core domain in complex with an inhibitor (2~{S})-2-[3-(3,4-dihydro-2~{H}-chromen-6-yl)-1-methyl-indol-2-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid Deposited 2016-06-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 7SK (2S)-tert-butoxy[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-1-methyl-1H-indol-2-yl]acetic acid × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；8%PEG 8K
.1M Ammonium Sulfate
.1M Na-cacodylate
5mM DTT
|
Resolution 2.67 Å R-free 0.244 |
| 5KRS HIV-1 Integrase Catalytic Core Domain in Complex with an Allosteric Inhibitor, 3-(1H-pyrrol-1-yl)-2-thiophenecarboxylic acid Deposited 2016-07-07 | 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
57–207（151 aa）
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | DMS DIMETHYL SULFOXIDE × 1 6XI 3-pyrrol-1-ylthiophene-2-carboxylic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；1 mM manganese chloride, 100 mM MES pH 6.7, 10% (w/v) PEG 8000, and 5 mM DTT
|
Resolution 1.70 Å R-free 0.186 |
| 5KRT HIV-1 Integrase Catalytic Core Domain (CCD) in Complex with a Fragment-Derived Allosteric Inhibitor Deposited 2016-07-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
57–207（151 aa）
Fragment：unp residues 57-207
|
Mutation：F185K Non-standard monomer：Yes (specific site not provided by mmCIF) | 6W6 3-[2,5-bis(chloranyl)pyrrol-1-yl]thiophene-2-carboxylic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；1 mM manganese chloride, 100 mM MES pH 6.7, 10% (w/v) PEG 8000, and 5 mM DTT
|
Resolution 1.65 Å R-free 0.195 |
| 6L0C Crystal structure of HIV-1 Integrase catalytic core domain (A128T/K173Q/F185K) Deposited 2019-09-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
|
Mutation：A128T, K173Q, F185K | SO4 SULFATE ION × 8 ARS ARSENIC × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；sodium cacodylate, ammonium sulfate
|
Resolution 2.10 Å R-free 0.240 |
| 6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18 | 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
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | CA CALCIUM ION × 4 ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å R-free 0.536 |
| 6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | CA CALCIUM ION × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å R-free 0.536 |
| 6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | CA CALCIUM ION × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å R-free 0.536 |
| 6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18 | 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
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 4 ZN ZINC ION × 4 KLQ Bictegravir × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å R-free 0.534 |
| 6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 KLQ Bictegravir × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å R-free 0.534 |
| 6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 KLQ Bictegravir × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å R-free 0.534 |
| 6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18 | 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
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 4 ZN ZINC ION × 4 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å R-free 0.516 |
| 6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-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
|
Resolution 2.80 Å R-free 0.516 |
| 6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-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
|
Resolution 2.80 Å R-free 0.516 |
| 6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18 | 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
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 4 ZN ZINC ION × 4 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å R-free 0.535 |
| 6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å R-free 0.535 |
| 6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å R-free 0.535 |
| 6U8Q CryoEM structure of HIV-1 cleaved synaptic complex (CSC) intasome Deposited 2019-09-05 | 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 × 12 PDB declaration: hexadecameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
Chain I
1–288（288 aa）
Chain J
1–288（288 aa）
Chain K
1–288（288 aa）
Chain L
1–288（288 aa）
Chain M
1–288（288 aa）
Chain N
1–288（288 aa）
Chain O
1–288（288 aa）
Chain P
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 4 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 4.67 Å |
| 6UM8 HIV Integrase in complex with Compound-14 Deposited 2019-10-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
57–212（156 aa）
Chain B
57–212（156 aa）
|
Not recorded | 1PE PENTAETHYLENE GLYCOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2 QCG (2S)-tert-butoxy[7-(8-fluoro-5-methyl-3,4-dihydro-2H-1-benzopyran-6-yl)-5-methyl-2-phenylpyrazolo[1,5-a]pyrimidin-6-yl]acetic acid × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.0 M ammonium sulfate and 100 mM citric acid pH 3.5
|
Resolution 2.33 Å R-free 0.220 |
| 6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25 | 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
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 4 ZN ZINC ION × 4 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å R-free 0.555 |
| 6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å R-free 0.555 |
| 6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–288（288 aa）
Chain B
1–288（288 aa）
Chain C
1–288（288 aa）
Chain D
1–288（288 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å R-free 0.555 |
| 6VQS HIV Integrase Core domain (IN) in complex with [5-(3-fluorophenyl)-1-benzofuran-3-yl]acetic acid Deposited 2020-02-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：core domain (UNP residues 50-212)
|
Not recorded | SO4 SULFATE ION × 6 IOD IODIDE ION × 8 R7J [5-(3-fluorophenyl)-1-benzofuran-3-yl]acetic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；2.2 M ammonium sulfate, 100 mM potassium iodide
|
Resolution 2.38 Å R-free 0.269 |
| 7L1P HIV Integrase Core domain (IN) in complex with dimer-spanning ligand Deposited 2020-12-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：UNP residues 50-212
Chain B
50–212（163 aa）
Fragment：UNP residues 50-212
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | R2A (2-{[3-(4-{2-[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzene-1-carbonyl)amino]ethyl}piperazine-1-carbonyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid × 1 IOD IODIDE ION × 6 SO4 SULFATE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；2.2 M ammonium sulfate, 100 mM potassium iodide
|
Resolution 1.85 Å R-free 0.284 |
| 7L23 HIV Integrase core domain in complex with inhibitor 2-(5-(3-fluorophenyl)-2-(2-(thiophen-2-yl)ethynyl)-1- benzofuran-3-yl)ethanoic acid Deposited 2020-12-16 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
57–206（150 aa）
Fragment：UNP residues 57-206
|
Not recorded | SO4 SULFATE ION × 4 IOD IODIDE ION × 10 XFS 3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；2.2 M ammonium sulfate, 100 mM potassium iodide
|
Resolution 2.26 Å R-free 0.280 |
| 7LQP Rapid development of potent inhibitors of the HIV integrase-LEDGF interaction by fragment-linking using off-rate screening Deposited 2021-02-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
57–212（156 aa）
Fragment：core domain (UNP residues 57-212)
Chain B
57–212（156 aa）
Fragment：core domain (UNP residues 57-212)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | IOD IODIDE ION × 6 SO4 SULFATE ION × 12 YAV 2-[2-[2-[3-[2-[2-[2-[[3-[2-[3-(2-hydroxy-2-oxoethyl)-5-methyl-1-benzofuran-2-yl]ethynyl]phenyl]carbonylamino]ethoxy]ethoxy]ethylcarbamoyl]phenyl]ethynyl]-5-methyl-1-benzofuran-3-yl]ethanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.2 M ammonium sulfate, 100 mM sodium iodide
|
Resolution 2.07 Å R-free 0.239 |
| 7RQ0 HIV Integrase CORE domain in complex with 2-{2-[2-(3-{[4-(2-{[(3-{2-[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)methyl]amino}ethyl)piperazin-1-yl]methyl}phenyl)ethynyl]-5-methyl-1-benzofuran-3-yl}acetic acid Deposited 2021-08-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：CORE domain (UNP residues 50-212)
Chain B
50–212（163 aa）
Fragment：CORE domain (UNP residues 50-212)
|
Not recorded | SO4 SULFATE ION × 6 IOD IODIDE ION × 5 6I2 {2-[(3-{[4-(2-{[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)methyl]amino}ethyl)piperazin-1-yl]methyl}phenyl)ethynyl]-5-methyl-1-benzofuran-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.2 M ammonium sulfate, pH 7.0, 100 mM potassium iodide
|
Resolution 1.95 Å R-free 0.270 |
| 7SIA HIV Integrase core domain in complex with inhibitor 2-[2-(2-{3-[(4-{2-[(3-{2-[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)formamido]ethyl}piperazin-1-yl)methyl]phenyl}ethynyl)-5-methyl-1-benzofuran-3-yl]acetic acid Deposited 2021-10-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
Fragment：core domain (UNP residues 50-212)
Chain B
50–212（163 aa）
Fragment：core domain (UNP residues 50-212)
|
Not recorded | 9I4 (2-{[3-({4-[2-(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzamido)ethyl]piperazin-1-yl}methyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid × 1 IOD IODIDE ION × 4 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.2 M ammonium sulfate, 100 mM potassium iodide
|
Resolution 1.85 Å R-free 0.264 |
| 7T9H HIV Integrase in complex with Compound-15 Deposited 2021-12-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
47–212（166 aa）
Chain B
47–212（166 aa）
|
Not recorded | MG MAGNESIUM ION × 2 GE7 (2S)-tert-butoxy[2-methyl-4-(4-methylphenyl)quinolin-3-yl]acetic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；4.6%(w/v) PEG 3350, 261 mM ammonium acetate, 0.81% glycerol(v/v), 91 mM magnesium chloride and 100 mM MES pH 6.0
|
Resolution 2.53 Å R-free 0.273 |
| 7T9O HIV Integrase in complex with Compound-25 Deposited 2021-12-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
47–209（163 aa）
|
Not recorded | SO4 SULFATE ION × 6 GEI (2S)-tert-butoxy[4-(4,4-dimethylpiperidin-1-yl)-5-{4-[2-(4-fluorophenyl)ethoxy]phenyl}-2,6-dimethylpyridin-3-yl]acetic acid × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；4.6%(w/v) PEG 3350, 261 mM ammonium acetate, 0.81% glycerol(v/v), 91 mM magnesium chloride and 100 mM MES pH 6.0
|
Resolution 1.95 Å R-free 0.219 |
| 7U2U CRYSTAL STRUCTURE OF HIV-1 INTEGRASE COMPLEXED WITH Compound-2a AKA (2S)-2-(TERT-BUTOXY)-2-[7-(4,4-DIMETHYLPIPE RIDIN-1-YL)-8-{4-[2-(4-FLUOROPHENYL)ETHOXY]PHENYL}-2,5-DIM ETHYLIMIDAZO[1,2-A]PYRIDIN-6-YL]ACETIC ACID Deposited 2022-02-24 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–209（160 aa）
|
Not recorded | KZD (2S)-tert-butoxy[(4S)-7-(4,4-dimethylpiperidin-1-yl)-8-{4-[2-(4-fluorophenyl)ethoxy]phenyl}-2,5-dimethylimidazo[1,2-a]pyridin-6-yl]acetic acid × 2 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2-0.18M Ammonium Sulfate, 100mM Na acetate pH 4.6-5.0
|
Resolution 1.84 Å R-free 0.211 |
| 8D3S HIV-1 Integrase Catalytic Core Domain F185H Mutant Complexed with BKC-110 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 monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
50–212（163 aa）
|
Mutation：F185H | 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 × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M ammonium sulfate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 10% PEG8000, 5 mM DTT
|
Resolution 1.84 Å R-free 0.274 |
| 8S9Q HIV-1 Integrase Catalytic Core Domain (CCD) F185H Mutant Complexed with STP03-0404 Deposited 2023-03-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–212（163 aa）
|
Not recorded | 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M (NH4)2SO4, 0.1 M sodium cacodylate (pH = 6.5), 10% PEG 8000, 5 mM DTT
|
Resolution 2.26 Å R-free 0.293 |
103 other PDB entries and 114 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | Q76353_9HIV1 |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 21–180； UniProt 50–209 |
