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1pro

HIV-1 PROTEASE DIMER COMPLEXED WITH A-98881

Method: X-RAY DIFFRACTION Dmax: 62.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HIV-1 PROTEASE

Human immunodeficiency virus 1

UniProt P12499

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 24–122 Chain B； UniProt 24–122 Not recorded A88 (5R,6R)-2,4-BIS-(4-HYDROXY-3-METHOXYBENZYL)-1,5-DIBENZYL-3-OXO-6-HYDROXY-1,2,4-TRIAZACYCLOHEPTANE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.80 Å R-free 0.310

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 1PRO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E28 Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant epitope KM2(TAFTIPSI) Deposited 2000-05-18 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 C 282–289（8 aa） Fragment：EXTRACELLULAR RESIDUES 282-289
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 3.00 Å R-free 0.253
1HXW HIV-1 PROTEASE DIMER COMPLEXED WITH A-84538 Deposited 1997-01-24 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–122（99 aa）
Chain B 24–122（99 aa）
Not recorded RIT RITONAVIR × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1P7Q Crystal Structure of HLA-A2 Bound to LIR-1, a Host and Viral MHC Receptor Deposited 2003-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 463–471（9 aa） Fragment：residue 463-471
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 4000, Sodium Acetate, Tris, L-Cysteine, Triton X-100, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.40 Å R-free 0.309
1Q94 Structures of HLA-A*1101 in complex with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle anchor residue Deposited 2003-08-22 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 C 745–753（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PEG 4000,sodium acetate,sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Resolution 2.40 Å R-free 0.272
1Q94 Structures of HLA-A*1101 in complex with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle anchor residue Deposited 2003-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 745–753（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PEG 4000,sodium acetate,sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Resolution 2.40 Å R-free 0.272
1VIJ HIV-1 PROTEASE COMPLEXED WITH THE INHIBITOR HOE/BAY 793 HEXAGONAL FORM Deposited 1997-05-07 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 56–154（99 aa）
Chain B 56–154（99 aa）
Not recorded BAY N-(1-BENZYL-2,3-DIHYDROXY-4-{3-METHYL-2-[2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYLAMINO]-BUTYRYLAMINO}-5-PHENYL-PENTYL)-3-METHYL-2-[2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYLAMINO]-BUTYRAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1VIK HIV-1 PROTEASE COMPLEXED WITH THE INHIBITOR HOE/BAY 793 ORTHORHOMBIC FORM Deposited 1997-05-07 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 56–154（99 aa）
Chain B 56–154（99 aa）
Not recorded BAY N-(1-BENZYL-2,3-DIHYDROXY-4-{3-METHYL-2-[2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYLAMINO]-BUTYRYLAMINO}-5-PHENYL-PENTYL)-3-METHYL-2-[2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYLAMINO]-BUTYRAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
3W39 Crystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI) Deposited 2012-12-13 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 C 716–723（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.347
3W39 Crystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI) Deposited 2012-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 716–723（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.347
4EJ8 Apo HIV Protease (PR) dimer in closed form with fragment 1F1 in the outside/top of flap Deposited 2012-04-06 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 490–588（99 aa） Fragment：UNP residues 490-588
Chain B 490–588（99 aa） Fragment：UNP residues 490-588
Mutation：Q7K, L33I, L63I, C67A, C95A Mutation：Q7K, L33I, L63I, C67A, C95A DMS DIMETHYL SULFOXIDE × 5 EDO 1,2-ETHANEDIOL × 4 1F1 1H-indole-6-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.1 M Tris, pH 7.5, 28% PEG4000, 10% DMSO, VAPOR DIFFUSION, temperature 298K
Resolution 2.35 Å R-free 0.243
4EJD HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1 in the outside/top of flap Deposited 2012-04-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 490–588（99 aa） Fragment：UNP residues 490-588
Chain B 490–588（99 aa） Fragment：UNP residues 490-588
Not recorded BME BETA-MERCAPTOETHANOL × 3 1F1 1H-indole-6-carboxylic acid × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；0.2 M potassium bromide, 0.2 M potassium thiocyanate, 3% PGA-LM, 3% MPD, 10% DMSO, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.10 Å R-free 0.176
4EJK HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1-N in the outside/top of flap Deposited 2012-04-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 490–588（99 aa） Fragment：UNP residues 490-588
Chain B 490–588（99 aa） Fragment：UNP residues 490-588
Not recorded IOP INDOLYLPROPIONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；298 K；1.0 M sodium formate, 10% DMSO, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, temperature 298K
Resolution 1.79 Å R-free 0.252
4EJL Apo HIV Protease (PR) dimer in closed form with fragment 1F1-N in the outside/top of flap Deposited 2012-04-06 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 490–588（99 aa） Fragment：UNP residues 490-588
Chain B 490–588（99 aa） Fragment：UNP residues 490-588
Mutation：Q7K, L33I, L63I, C67A, C95A Mutation：Q7K, L33I, L63I, C67A, C95A PEG DI(HYDROXYETHYL)ETHER × 1 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 4 IOP INDOLYLPROPIONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；298 K；0.8 M sodium formate, 15% PEG4000, 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.44 Å R-free 0.245
4K4P TL-3 inhibited Trp6Ala HIV Protease Deposited 2013-04-12 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 1–99（99 aa）
Chain B 1–99（99 aa）
Mutation：W6A Mutation：W6A NO3 NITRATE ION × 1 3TL benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；0.1M NaOAc pH 5.0, 2.5M NaNO3, vapor diffusion, temperature 298K
Resolution 2.31 Å R-free 0.234
4K4Q TL-3 inhibited Trp6Ala HIV Protease with 3-bromo-2,6-dimethoxybenzoic acid bound in flap site Deposited 2013-04-12 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 1–99（99 aa）
Chain B 1–99（99 aa）
Mutation：W6A Mutation：W6A NO3 NITRATE ION × 6 BME BETA-MERCAPTOETHANOL × 1 DMS DIMETHYL SULFOXIDE × 2 3TL benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate × 1 06B 3-bromo-2,6-dimethoxybenzoic acid × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；0.1M NaOAc pH 5.0, 2.5M NaNO3, vapor diffusion, temperature 298K
Resolution 1.80 Å R-free 0.230
4K4R TL-3 inhibited Trp6Ala HIV Protease with 1-bromo-2-napthoic acid bound in exosite Deposited 2013-04-12 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 1–99（99 aa）
Chain B 1–99（99 aa）
Mutation：W6A Mutation：W6A DMS DIMETHYL SULFOXIDE × 1 27B 1-bromonaphthalene-2-carboxylic acid × 2 NO3 NITRATE ION × 5 3TL benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate × 1 BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；0.1M NaOAc pH 5.0, 2.5M NaNO3, vapor diffusion, temperature 298K
Resolution 1.80 Å R-free 0.235
9K2R Human T cell receptor (TRAV24*01/TRBV27*01) in complex with HLA-C*1202 and IY11 peptide Deposited 2024-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 897–907（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.0, 1.6M ammonium sulfate, 0.2M sodium thiocyanate
Resolution 2.98 Å R-free 0.233
9K2R Human T cell receptor (TRAV24*01/TRBV27*01) in complex with HLA-C*1202 and IY11 peptide Deposited 2024-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 897–907（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.0, 1.6M ammonium sulfate, 0.2M sodium thiocyanate
Resolution 2.98 Å R-free 0.233
9K2R Human T cell receptor (TRAV24*01/TRBV27*01) in complex with HLA-C*1202 and IY11 peptide Deposited 2024-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 897–907（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.0, 1.6M ammonium sulfate, 0.2M sodium thiocyanate
Resolution 2.98 Å R-free 0.233
9K2S Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*1202 and IY10 peptide Deposited 2024-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 897–906（10 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M K/Na tartrate, 20% PEG 3350
Resolution 2.40 Å R-free 0.299
9K2T Crystal structure of HLA-C*1202 in complex with IY10 peptide Deposited 2024-10-18 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 C 897–906（10 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；PEG
Resolution 2.20 Å R-free 0.243

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POL_HV1Z2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–99； UniProt 24–122 Author chain B； PDBConstruct 1–99； UniProt 24–122

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1pro

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pro
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1pro
Deposition date deposition_date1995-07-18
Structure title titleHIV-1 PROTEASE DIMER COMPLEXED WITH A-98881
Keywords keywordsAIDS, POLYPROTEIN, HYDROLASE, ASPARTIC PROTEASE, ENDONUCLEASE, RNA-DIRECTED DNA POLYMERASE, HYDROLASE (ASPARTIC PROTEASE); HYDROLASE (ASPARTIC PROTEASE)
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.32 Å
Radius of gyration Rg (electron density) rg_electron17.31 Å
Forward intensity I(0) i07992000.00
Molecular weight molecular_weight22227.0 kDa
Excluded volume excluded_volume28532 ų
Envelope volume envelope_volume31793 ų
Hydration-shell volume shell_volume15746 ų
Envelope diameter envelope_diameter62.3 Å
Shell Rg shell_rg23.12 Å
Envelope Rg envelope_rg17.67 Å
Shape Rg shape_rg17.30 Å
Total Rg total_rg18.36 Å
Total atoms total_atoms1563
Residues n_residues198
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax62.1 Å
Rg (real space) rg_real18.30 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real7.9920e+06
I(0) uncertainty (real space) i0_real_error9.5690e+04
Rg (reciprocal space) rg_reciprocal18.30 Å
I(0) (reciprocal space) i0_reciprocal7992000.0000
Solution quality estimate total_estimate0.8666
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.1 Å
Skewness Skewness skewness0.358
Kurtosis Kurtosis kurtosis-0.247
Angular range angular_range— – 0.4350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3245000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.958
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1proa_
Class classb — All beta proteins
Fold Fold foldb.50 — Acid proteases
Superfamily Superfamily superfamilyb.50.1 — Acid proteases
Family Family familyb.50.1.1 — Retroviral protease (retropepsin)
Domain ID domain_idd1prob_
Class classb — All beta proteins
Fold Fold foldb.50 — Acid proteases
Superfamily Superfamily superfamilyb.50.1 — Acid proteases
Family Family familyb.50.1.1 — Retroviral protease (retropepsin)

CATH v4.4 (2 domains)

Domain ID domain_id1proA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
Domain ID domain_id1proB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
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8. Citations (1)

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9. Files and Curves (10)