SAXSdb — 2i4d

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protease

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 500–598 Chain B； UniProt 500–598	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

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 2I4D	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 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） 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 construct 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
1GNM HIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASP (V82D) COMPLEXED WITH U89360E (INHIBITOR) Deposited 1996-05-04	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 69–167（99 aa） Chain B 69–167（99 aa）	Mutation：V82D 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 conditions	Resolution 2.30 Å
1GNN HIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASN (V82N) COMPLEXED WITH U89360E (INHIBITOR) Deposited 1996-05-04	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 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 construct 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	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 construct 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	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 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 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 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 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 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 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
2I4U HIV-1 protease with TMC-126 Deposited 2006-08-22	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 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 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 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 500–598 Author chain B； PDBConstruct 1–99； UniProt 500–598

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2i4d
Deposition date deposition_date	2006-08-21
Structure title title	Crystal structure of WT HIV-1 protease with GS-8373
Keywords keywords	HIV-1 Protease, hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.01 Å
Radius of gyration Rg (electron density) rg_electron	17.11 Å
Forward intensity I(0) i0	8115880.00
Molecular weight molecular_weight	22318.0 kDa
Excluded volume excluded_volume	28606 Å³
Envelope volume envelope_volume	31503 Å³
Hydration-shell volume shell_volume	15759 Å³
Envelope diameter envelope_diameter	59.9 Å
Shell Rg shell_rg	22.88 Å
Envelope Rg envelope_rg	17.40 Å
Shape Rg shape_rg	17.12 Å
Total Rg total_rg	18.06 Å
Total atoms total_atoms	1565
Residues n_residues	198
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	59.8 Å
Rg (real space) rg_real	17.98 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	8.1160e+06
I(0) uncertainty (real space) i0_real_error	9.4890e+04
Rg (reciprocal space) rg_reciprocal	17.98 Å
I(0) (reciprocal space) i0_reciprocal	8116000.0000
Solution quality estimate total_estimate	0.8685
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.339
Kurtosis Kurtosis kurtosis	-0.249
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3073000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.881

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protease
Molecular weight formula_weight	10831.8 kDa
EC 编号 ec_number	3.4.23.16
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1739

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGMTLNF

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;({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 ;
Molecular weight formula_weight	672.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	174

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2i4da_
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.1 — Retroviral protease (retropepsin)

Domain ID domain_id	d2i4db_
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.1 — Retroviral protease (retropepsin)

CATH v4.4 (2 domains)

Domain ID domain_id	2i4dA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

Domain ID domain_id	2i4dB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

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8. Citations (1)

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Unit-cell length a length_a	57.422 Å
Unit-cell length b length_b	86.114 Å
Unit-cell length c length_c	46.165 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.2410
R_free r_free	0.2740

fit	/app/data/saxs_computation/i4/2i4d/2i4d.fit
pddf	/app/data/pr_computation/i4/2i4d/2i4d.pr.out
profile	/app/data/saxs_computation/i4/2i4d/2i4d.dat

Crystal structure of WT HIV-1 protease with GS-8373

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protease

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction