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1gnm

HIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASP (V82D) COMPLEXED WITH U89360E (INHIBITOR)

Method: X-RAY DIFFRACTION Dmax: 59.8 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 P03368

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 69–167 Chain B； UniProt 69–167 Mutation：V82D U0E N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.30 Å

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 1GNM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A9M G48H MUTANT OF HIV-1 PROTEASE IN COMPLEX WITH A PEPTIDIC INHIBITOR U-89360E Deposited 1998-04-08 Different mutation/modification Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 69–167（99 aa）
Chain B 69–167（99 aa）
Mutation：G48H Mutation：G48H U0E N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；THE PROTEIN SOLUTION CONTAINED 6.5 MG/ML MUTANT HIV-1 PROTEASE IN 20 MM SODIUM ACETATE, 1 MM DITHIOTHREITOL, PH 5.5, WITH A 10-FOLD MOLAR EXCESS OF INHIBITOR. THE RESERVOIR SOLUTIONS FOR THE VAPOR DIFFUSION CONTAINED 10% DIMETHYLSULFOXIDE, 30 MM B-MERCAPTOETHANOL AND 4% 2-PROPANOL IN ADDITION TO THE PRECIPITANT. THE MOST FAVORABLE CRYSTALLIZATION CONDITIONS WERE 42% SATURATED AMMONIUM SULFATE, PH 6.8., vapor diffusion
Resolution 2.30 Å
1G35 CRYSTAL STRUCTURE OF HIV-1 PROTEASE IN COMPLEX WITH INHIBITOR, AHA024 Deposited 2000-10-23 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 69–167（99 aa）
Chain B 69–167（99 aa）
Not recorded AHF 2-[4-(HYDROXY-METHOXY-METHYL)-BENZYL]-7-(4-HYDROXYMETHYL-BENZYL)-1,1-DIOXO-3,6-BIS-PHENOXYMETHYL-1LAMBDA6-[1,2,7]THIADIAZEPANE-4,5-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；50 mM MES, 0.4 M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.230
1GNN HIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASN (V82N) COMPLEXED WITH U89360E (INHIBITOR) Deposited 1996-05-04 Different mutation/modification Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 69–167（99 aa）
Chain B 69–167（99 aa）
Mutation：V82N Mutation：V82N U0E N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1GNO HIV-1 PROTEASE (WILD TYPE) COMPLEXED WITH U89360E (INHIBITOR) Deposited 1996-05-04 Different mutation/modification Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 69–167（99 aa）
Chain B 69–167（99 aa）
Not recorded U0E N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1HVI INFLUENCE OF STEREOCHEMISTRY ON ACTIVITY AND BINDING MODES FOR C2 SYMMETRY-BASED DIOL INHIBITORS OF HIV-1 PROTEASE Deposited 1994-01-26 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 69–167（99 aa）
Chain B 69–167（99 aa）
Not recorded A77 N-{1-BENZYL-(2R,3S)-2,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1KJH SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES Deposited 2001-12-04 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 P 723–732（10 aa） Fragment：RNASE H-INTEGRASE SUBSTRATE PEPTIDE, RESIDUES 723-732
Not recorded ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；AMMONIUM SULPHATE, SODIUM CITRATE, SODIUM PHOSPHATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.227
1NPA crystal structure of HIV-1 protease-hup Deposited 2003-01-17 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 69–167（99 aa） Fragment：protease, residue 69-167
Chain B 69–167（99 aa） Fragment：protease, residue 69-167
Not recorded 3NH (3S)-TETRAHYDROFURAN-3-YL (1R,2S)-3-[4-((1R)-2-{[(S)-AMINO(HYDROXY)METHYL]OXY}-2,3-DIHYDRO-1H-INDEN-1-YL)-2-BENZYL-3-OXOPYRROLIDIN-2-YL]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；0.1 M NaAc, 0.5 M NaCl, 1mM DTT, 3mM NaN3, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å
1NPV Crystal structure of HIV-1 protease complexed with LDC271 Deposited 2003-01-20 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 69–167（99 aa） Fragment：HIV protease
Chain B 69–167（99 aa） Fragment：HIV protease
Not recorded L27 {1-BENZYL-3-[2-BENZYL-3-OXO-4-(1-OXO-1,2,3,4-TETRAHYDRO- ISOQUINOLIN-4-YL)-2,3-DIHYDRO-1H-PYRROL-2-YL]-2- HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；600mM NaCl, 100mM Sodium Acetate buffer at pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.260
1NPW Crystal structure of HIV protease complexed with LGZ479 Deposited 2003-01-20 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 69–167（99 aa） Fragment：HIV-1 PROTEASE
Chain B 69–167（99 aa） Fragment：HIV-1 PROTEASE
Not recorded LGZ CARBAMIC ACID 1-{5-BENZYL-5-[2-HYDROXY-4-PHENYL-3-(TETRAHYDRO-FURAN- 3-YLOXYCARBONYLAMINO)-BUTYL]-4-OXO-4,5-DIHYDRO-1H-PYRROL-3-YL}- INDAN-2-YL ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；600mM NaCl, 100mM Sodium Acetate buffer, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å
1T7K Crystal Structure of HIV Protease complexed with Arylsulfonamide azacyclic urea Deposited 2004-05-10 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 69–167（99 aa） Fragment：HIV Protease
Chain B 69–167（99 aa） Fragment：HIV Protease
Not recorded BH0 3-({5-BENZYL-6-HYDROXY-2,4-BIS-(4-HYDROXY-BENZYL)-3-OXO-[1,2,4]-TRIAZEPANE-1-SULFONYL)-BENZONITRILE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；293 K；0.1M sodium acetate, 0.6M NaCl, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.277
1YT9 HIV Protease with oximinoarylsulfonamide bound Deposited 2005-02-10 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 69–167（99 aa） Fragment：HIV protease
Chain B 69–167（99 aa） Fragment：HIV protease
Not recorded OIS (S)-N-((2S,3R)-3-HYDROXY-4-(4-((E)-(HYDROXYIMINO)METHYL)-N-ISOBUTYLPHENYLSULFONAMIDO)-1-PHENYLBUTAN-2-YL)-3-METHYL-2-(3 -((2-METHYLTHIAZOL-4-YL)METHYL)-2-OXOIMIDAZOLIDIN-1-YL)BUTANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；nacl, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.338
1ZP8 HIV Protease with inhibitor AB-2 Deposited 2005-05-16 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 69–167（99 aa） Fragment：HIV Protease
Not recorded AB2 [1-((1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL)-1H-1,2,3-TRIAZOL-4-YL]METHYL (1R,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YLCARBAMATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；1.34 M Ammonium Sulfate, 0.1 M Na Acetate, pH 4.8-5.4, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.02 Å R-free 0.326
1ZPA HIV Protease with Scripps AB-3 Inhibitor Deposited 2005-05-16 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 69–167（99 aa） Fragment：HIV Protease
Not recorded A83 TERT-BUTYL 4-[({[1-((1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL)-1H-1,2,3-TRIAZOL-4-YL]METHYL}AMINO)CARBONYL]BENZYLCARBAMATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；1.34 M Ammonium Sulfate, 0.1 M Na Acetate, pH 4.8-5.4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.02 Å
2EXF Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site Deposited 2005-11-08 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 Monomer；Protein × 1 PDB declaration: dimeric
Chain A 389–431（43 aa）
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；283 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide；Pressure ambient
NMR measurement conditions pH 6.5；283 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2；Pressure ambient
NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide；Pressure ambient
NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2；Pressure ambient
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide；Pressure ambient
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 1mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2；Pressure ambient
NMR sample composition 1mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2 | 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2
NMR sample composition 2mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 2mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2 | 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2
Resolution not provided
2FDE Wild type HIV protease bound with GW0385 Deposited 2005-12-13 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 500–598（99 aa） Fragment：protease
Chain B 500–598（99 aa） Fragment：protease
Not recorded K POTASSIUM ION × 4 385 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(1S,2R)-3-[(1,3-BENZODIOXOL-5-YLSULFONYL)(ISOBUTYL)AMINO]-2-HYDROXY-1-{4-[(2-METHYL-1,3-THIAZOL-4-YL)METHOXY]BENZYL}PROPYL]CARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.280
2G69 Structure of Unliganded HIV-1 Protease F53L Mutant Deposited 2006-02-24 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 1–99（99 aa） Fragment：HIV-1 protease monomer
Mutation：Q7K, L33I, F53L, L63I, C67A, C95A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；The reservoir contained 0.2 M sodium citrate, phosphate buffer (pH = 6.0-6.4), 10% DMSO, and 20-30% saturated ammonium sulfate as a precipitant., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.35 Å R-free 0.234
2HNZ Crystal Structure of E138K Mutant HIV-1 Reverse Transcriptase in Complex with PETT-2 Deposited 2006-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 605–1026（422 aa） Fragment：P51
Mutation：E138K PO4 PHOSPHATE ION × 2 PC0 1-[2-(4-ETHOXY-3-FLUOROPYRIDIN-2-YL)ETHYL]-3-(5-METHYLPYRIDIN-2-YL)THIOUREA × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.00 Å R-free 0.277
2HS1 Ultra-high resolution X-ray crystal structure of HIV-1 protease V32I mutant with TMC114 (darunavir) inhibitor Deposited 2006-07-20 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 500–598（99 aa） Fragment：HIV-1 protease (residues 500-598)
Chain B 500–598（99 aa） Fragment：HIV-1 protease (residues 500-598)
Mutation：Q7K, V32I, L33I, L63I, C67A, C95A Mutation：Q7K, V32I, L33I, L63I, C67A, C95A CL CHLORIDE ION × 3 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；1-1.5 M NaCl; Molar Protein:Inhibitor ratio = 1:20, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 0.84 Å R-free 0.149
2HS2 Crystal structure of M46L mutant of HIV-1 protease complexed with TMC114 (darunavir) Deposited 2006-07-20 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 500–598（99 aa） Fragment：HIV-1 protease (residues 500-598)
Chain B 500–598（99 aa） Fragment：HIV-1 protease (residues 500-598)
Mutation：Q7K, L33I, M46L, L63I, C67A, C95A Mutation：Q7K, L33I, M46L, L63I, C67A, C95A CL CHLORIDE ION × 2 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；295 K；25% NaCl; Molar protein:inhibitor ratio 1:2., pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.22 Å R-free 0.195
2I4D Crystal structure of WT HIV-1 protease with GS-8373 Deposited 2006-08-21 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 500–598（99 aa）
Chain B 500–598（99 aa）
Not recorded QFI ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2M Mg Acetate, 0.1M Na cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.274
2I4U HIV-1 protease with TMC-126 Deposited 2006-08-22 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 500–598（99 aa）
Chain B 500–598（99 aa）
Not recorded DJR (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]CARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.4 M Sodium Potassium Tartrate, pH 7.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.50 Å R-free 0.250
2I4V HIV-1 protease I84V, L90M with TMC126 Deposited 2006-08-22 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 500–598（99 aa）
Chain B 500–598（99 aa）
Mutation：I84V, L90M Mutation：I84V, L90M DJR (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]CARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.4 M Sodium Potassium Tartrate, pH 7.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.50 Å R-free 0.256
2I4W HIV-1 protease WT with GS-8374 Deposited 2006-08-22 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 500–598（99 aa）
Chain B 500–598（99 aa）
Not recorded KGQ DIETHYL ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；0.2M Mg Acetate, 0.1M Na Cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.55 Å R-free 0.252
2I4X HIV-1 Protease I84V, L90M with GS-8374 Deposited 2006-08-22 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 500–598（99 aa）
Chain B 500–598（99 aa）
Mutation：I84V, L90M Mutation：I84V, L90M KGQ DIETHYL ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.4 M Sodium Potassium Tartrate, pH 7.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.55 Å R-free 0.272
2IDW Crystal structure analysis of HIV-1 protease mutant V82A with a potent non-peptide inhibitor (UIC-94017) Deposited 2006-09-15 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 500–598（99 aa） Fragment：residues 500-598
Chain B 500–598（99 aa） Fragment：residues 500-598
Mutation：Q7K, L33I, L63I, C67A, V82A, C95A, Q107K, L133I, L163I, C167A, V182A, C195A Mutation：Q7K, L33I, L63I, C67A, V82A, C95A, Q107K, L133I, L163I, C167A, V182A, C195A CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 4 DMS DIMETHYL SULFOXIDE × 1 ACY ACETIC ACID × 6 GOL GLYCEROL × 1 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；AMMONIUM SULFATE, CITRIC PHOSPHATE, DMSO, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.10 Å R-free 0.145
2IEN Crystal structure analysis of HIV-1 protease with a potent non-peptide inhibitor (UIC-94017) Deposited 2006-09-19 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 500–598（99 aa） Fragment：residues 500-598
Chain B 500–598（99 aa） Fragment：residues 500-598
Mutation：Q7K, L33I, L63I, C67A, C95A, Q107K, L133I, L163I, C167A, C195A Mutation：Q7K, L33I, L63I, C67A, C95A, Q107K, L133I, L163I, C167A, C195A NA SODIUM ION × 1 CL CHLORIDE ION × 2 ACY ACETIC ACID × 2 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；sodium chloride, sodium acetate, DMSO, dioxane, pH 4.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.30 Å R-free 0.205
2IEO Crystal structure analysis of HIV-1 protease mutant I84V with a potent non-peptide inhibitor (UIC-94017) Deposited 2006-09-19 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 500–598（99 aa） Fragment：residues 500-598
Chain B 500–598（99 aa） Fragment：residues 500-598
Mutation：Q7K, L33I, L63I, C67A, I84V, C95A, Q107K, L133I, L163I, C167A, C195A Mutation：Q7K, L33I, L63I, C67A, I84V, C95A, Q107K, L133I, L163I, C167A, C195A CL CHLORIDE ION × 3 NA SODIUM ION × 1 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；SODIUM CHLORIDE, CITRATE PHOSPHATE, DMSO, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.53 Å R-free 0.196

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POL_HV1PV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–99； UniProt 69–167 Author chain B； PDBConstruct 1–99； UniProt 69–167

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 1gnm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1gnm
Deposition date deposition_date1996-05-04
Structure title titleHIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASP (V82D) COMPLEXED WITH U89360E (INHIBITOR)
Keywords keywordsASPARTIC PROTEASE, HIV, MUTANT, INHIBITOR, U-89360E, HYDROLASE (ACID PROTEASE); HYDROLASE (ACID 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_guinier18.03 Å
Radius of gyration Rg (electron density) rg_electron17.10 Å
Forward intensity I(0) i08453140.00
Molecular weight molecular_weight22813.0 kDa
Excluded volume excluded_volume29225 ų
Envelope volume envelope_volume32144 ų
Hydration-shell volume shell_volume15975 ų
Envelope diameter envelope_diameter61.7 Å
Shell Rg shell_rg23.02 Å
Envelope Rg envelope_rg17.54 Å
Shape Rg shape_rg17.10 Å
Total Rg total_rg18.09 Å
Total atoms total_atoms1602
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 dmax59.8 Å
Rg (real space) rg_real18.01 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real8.4530e+06
I(0) uncertainty (real space) i0_real_error1.0980e+05
Rg (reciprocal space) rg_reciprocal18.01 Å
I(0) (reciprocal space) i0_reciprocal8453000.0000
Solution quality estimate total_estimate0.7961
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.0 Å
Skewness Skewness skewness0.366
Kurtosis Kurtosis kurtosis-0.200
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3537000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.783; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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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_idd1gnma_
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_idd1gnmb_
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_id1gnmA00
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_id1gnmB00
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 (2)

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9. Files and Curves (10)