1hsh

CRYSTAL STRUCTURE AT 1.9 ANGSTROMS RESOLUTION OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) II PROTEASE COMPLEXED WITH L-735,524, AN ORALLY BIOAVAILABLE INHIBITOR OF THE HIV PROTEASES

Method: X-RAY DIFFRACTION D_max: 86.2 Å Quality: GOOD

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

HIV-II PROTEASE

Human immunodeficiency virus 2

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 86–184 Chain B； UniProt 86–184	Not recorded	MK1 N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 86–184 Chain D； UniProt 86–184	Not recorded	MK1 N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 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 1HSH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E0E N-terminal zinc-binding HHCC domain of HIV-2 integrase Deposited 2000-03-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 744–798（55 aa） Fragment：N-TERMINAL HHCC DOMAIN Chain B 744–798（55 aa） Fragment：N-TERMINAL HHCC DOMAIN	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 6.5；300 K NMR sample composition D2O AND 5% D2O/95% H2O	Resolution not provided
1HII COMPARATIVE ANALYSIS OF THE X-RAY STRUCTURES OF HIV-1 AND HIV-2 PROTEASES IN COMPLEX WITH CGP 53820, A NOVEL PSEUDOSYMMETRIC INHIBITOR Deposited 1995-03-31	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 86–184（99 aa） Chain B 86–184（99 aa）	Not recorded	SO4 SULFATE ION × 2 C20 ACETYL-NH-VAL-CYCLOHEXYL-CH2[NCH2CHOH]CH2-BENZYL-VAL-NH-ACETYL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1HSI CRYSTAL STRUCTURE AT 1.9 ANGSTROMS RESOLUTION OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) II PROTEASE COMPLEXED WITH L-735,524, AN ORALLY BIOAVAILABLE INHIBITOR OF THE HIV PROTEASES Deposited 1995-03-31	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 86–184（99 aa） Chain B 86–184（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1IDA CRYSTAL STRUCTURES OF HIV-2 PROTEASE IN COMPLEX WITH INHIBITORS CONTAINING THE HYDROXYETHYLAMINE DIPEPTIDE ISOSTERE Deposited 1994-10-19	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 514–612（99 aa） Fragment：rsidues 514-622 Chain B 514–612（99 aa） Fragment：rsidues 514-622	Not recorded	0PO N-[(1R)-1-{[(1S,2S)-1-benzyl-3-{(2R,4S)-2-(tert-butylcarbamoyl)-4-[(pyridin-3-ylmethyl)sulfanyl]piperidin-1-yl}-2-hydroxypropyl]carbamoyl}-2-methylpropyl]quinoline-2-carboxamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1IVP THE CRYSTALLOGRAPHIC STRUCTURE OF THE PROTEASE FROM HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 WITH TWO SYNTHETIC PEPTIDIC TRANSITION STATE ANALOG INHIBITORS Deposited 1993-03-18	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 86–184（99 aa） Chain B 86–184（99 aa）	Not recorded	1ZK 4-[(2R)-3-{[(1S,2S,3R,4S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methyl-4-({(1S,2R)-2-methyl-1-[(pyridin-2-ylmethyl)carba moyl]butyl}carbamoyl)hexyl]amino}-2-{[(naphthalen-1-yloxy)acetyl]amino}-3-oxopropyl]-1H-imidazol-3-ium × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1IVQ THE CRYSTALLOGRAPHIC STRUCTURE OF THE PROTEASE FROM HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 WITH TWO SYNTHETIC PEPTIDIC TRANSITION STATE ANALOG INHIBITORS Deposited 1993-03-18	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 86–184（99 aa） Chain B 86–184（99 aa）	Not recorded	0PX N~1~-{(1S,2S,4S)-1-(cyclohexylmethyl)-4-[(2,2-dimethylpropyl)carbamoyl]-2-hydroxy-5-methylhexyl}-N~2~-(quinolin-2-ylcar bonyl)-L-aspartamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1MU2 CRYSTAL STRUCTURE OF HIV-2 REVERSE TRANSCRIPTASE Deposited 2002-09-23	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 185–739（555 aa） Chain B 190–615（426 aa） Fragment：residues 6-431	Mutation：R286S Mutation：R286S	SO4 SULFATE ION × 22 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；(NH4)2SO4, TRIS, DMSO, GLYCEROL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.35 Å R-free 0.240
2HPE COMPARISON OF THE STRUCTURES OF HIV-2 PROTEASE COMPLEXES IN THREE CRYSTAL SPACE GROUPS WITH AN HIV-1 PROTEASE COMPLEX STRUCTURE Deposited 1994-09-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 86–184（99 aa） Chain B 86–184（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
2HPF COMPARISON OF THE STRUCTURES OF HIV-2 PROTEASE COMPLEXES IN THREE CRYSTAL SPACE GROUPS WITH AN HIV-1 PROTEASE COMPLEX STRUCTURE Deposited 1994-09-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 86–184（99 aa） Chain B 86–184（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2K4E Solution structure of the HIV-2 UNMYRISTOYLATED MATRIX PROTEIN Deposited 2008-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–135（134 aa） Fragment：UNP residues 2 to 135	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；308 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.8 mM [U-15N] HIV-2 unmyristoylated matrix protein, 20 mM potassium phosphate, 10 mM DTT, 50 mM Glutamate, 50 mM Aspartate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM HIV-2 unmyristoylated matrix protein, 100% D2O \| 100% D2O NMR sample composition 0.8 mM [U-13C; U-15N] HIV-2 unmyristoylated matrix protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K4H Solution structure of the HIV-2 myristoylated Matrix protein Deposited 2008-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–135（134 aa） Fragment：UNP residues 2 to 135	Not recorded	MYR MYRISTIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 6.3；308 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.8 mM [U-15N] HIV-2 myristoylated matrix protein, 20 mM potassium phosphate, 10 mM DTT, 50 mM Glutamate, 50 mM Aspartate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM HIV-2 myristoylated matrix protein, 100% D2O \| 100% D2O NMR sample composition 0.8 mM [U-13C; U-15N] HIV-2 myristoylated matrix protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K4I Solution structure of HIV-2 myrMA bound to di-C4-PI(4,5)P2 Deposited 2008-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–135（134 aa） Fragment：UNP residues 2 to 135	Not recorded	MYR MYRISTIC ACID × 1 PBU (2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1 ,2-DIYL DIBUTANOATE × 1	SOLUTION NMR NMR measurement conditions pH 6.3；308 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.8 mM [U-15N] HIV-2 myristoylated matrix protein, 20 mM potassium phosphate, 10 mM DTT, 50 mM Glutamate, 50 mM Aspartate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM HIV-2 myristoylated matrix protein, 100% D2O \| 100% D2O NMR sample composition 0.8 mM [U-13C; U-15N] HIV-2 myristoylated matrix protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MIP CRYSTAL STRUCTURE OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) TYPE 2 PROTEASE IN COMPLEX WITH A REDUCED AMIDE INHIBITOR AND COMPARISON WITH HIV-1 PROTEASE STRUCTURES Deposited 1993-06-03	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 86–184（99 aa） Chain B 86–184（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
2MIP CRYSTAL STRUCTURE OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) TYPE 2 PROTEASE IN COMPLEX WITH A REDUCED AMIDE INHIBITOR AND COMPARISON WITH HIV-1 PROTEASE STRUCTURES Deposited 1993-06-03	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 86–184（99 aa） Chain D 86–184（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
3EBZ High Resolution HIV-2 Protease Structure in Complex with Clinical Drug Darunavir Deposited 2008-08-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 514–612（99 aa） Chain B 514–612（99 aa）	Not recorded	IMD IMIDAZOLE × 6 ZN ZINC ION × 9 CL CHLORIDE ION × 8 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 5.75；293 K；0.6-0.7M imidazole, 0.12-0.14M Zn(OAc)2 buffer, 1.25-2M NaCl, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.20 Å R-free 0.181
3EC0 High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-06579A Deposited 2008-08-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 514–612（99 aa） Chain B 514–612（99 aa）	Not recorded	GRL (3AS,5R,6AR)-HEXAHYDRO-2H-CYCLOPENTA[B]FURAN-5-YL (2S,3S)-3-HYDROXY-4-(4-(HYDROXYMETHYL)-N-ISOBUTYLPHENYLSULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE × 1 IMD IMIDAZOLE × 6 ZN ZINC ION × 10 CL CHLORIDE ION × 8 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；0.6-0.7M imidazole, 0.12-0.14M Zn(OAc)2 buffer, 1.25-2M NaCl, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.18 Å R-free 0.206
3ECG High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-98065 Deposited 2008-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 514–612（99 aa） Chain B 514–612（99 aa）	Not recorded	065 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(2S,3R)-3-HYDROXY-4-(N-ISOBUTYLBENZO[D][1,3]DIOXOLE-5-SULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE × 1 IMD IMIDAZOLE × 6 ZN ZINC ION × 11 CL CHLORIDE ION × 9 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；0.6-0.7M imidazole, 0.12-0.14M Zn(OAc)2 buffer, 1.25-2M NaCl, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.18 Å R-free 0.188
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	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 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain B 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain k 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain l 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain o 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain p 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain s 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain t 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain E 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain F 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain U 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain V 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain g 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain h 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain B 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain I 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain J 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain Y 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain Z 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain k 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain l 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain o 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain p 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain s 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain t 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain M 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain N 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain Q 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain R 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain c 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain d 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain F 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain J 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain N 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Q 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain R 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain U 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain V 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain Z 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain c 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain d 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain g 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380 Chain h 1173–1380（208 aa） Fragment：N-terminal and catalytic domains, UNP residues 1173-1380	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.234
3UPJ HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 PROTEASE MUTANT WITH LYS 57 REPLACED BY LEU (K57L) COMPLEX WITH U096333 [4-HYDROXY-3-[1-(PHENYL)PROPYL]-7-METHOXYCOUMARIN] Deposited 1996-03-04	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 86–184（99 aa） Chain B 86–184（99 aa）	Mutation：K57L Mutation：K57L	U03 4-HYDROXY-7-METHOXY-3-(1-PHENYL-PROPYL)-CHROMEN-2-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.50 Å
4UPJ HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 PROTEASE MUTANT WITH LYS 57 REPLACED BY LEU (K57L) COMPLEX WITH U097410 [4-HYDROXY-3-[1-[3-[[[[(TERT-BUTYLOXYCARBONYL) AMINOMETHYL]CARBONYL]AMINO]PHENYL]PROPYL]COUMARIN Deposited 1996-03-04	Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 86–184（99 aa） Chain B 86–184（99 aa）	Mutation：K57L Mutation：K57L	U04 ({3-[1-(4-HYDROXY-2-OXO-2H-CHROMEN-3-YL)-PROPYL]-PHENYLCARBAMOYL}-METHYL)-CARBAMIC ACID TERT-BUTYL ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 1.90 Å
5UPJ HIV-2 PROTEASE/U99283 COMPLEX Deposited 1996-12-10	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 86–184（99 aa） Chain B 86–184（99 aa）	Mutation：K57L Mutation：K57L	UIN 5,6,7,8,9,10-HEXAHYDRO-4-HYDROXY-3-(1-PHENYLPROPYL)CYCLOOCTA[B]PYRAN-2-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 4-7 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN AT 8-10 MG/L AND WELL SOLUTION OF 30-35%(W/V) PEG 4000 IN 0.1 M HEPES AND PH RANGE 6.8 - 7.6., pH 7.1, vapor diffusion - hanging drop	Resolution 2.30 Å
6UPJ HIV-2 PROTEASE/U99294 COMPLEX Deposited 1996-12-10	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 86–184（99 aa） Chain B 86–184（99 aa）	Mutation：K57L Mutation：K57L	NIU 6,7,8,9-TETRAHYDRO-4-HYDROXY-3-(1-PHENYLPROPYL)CYCLOHEPTA[B]PYRAN-2-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 4-7 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN AT 8-10 MG/L AND WELL SOLUTION OF 30-35%(W/V) PEG 4000 IN 0.1 M HEPES AND PH RANGE 6.8 - 7.6., pH 7.0, vapor diffusion - hanging drop	Resolution 2.34 Å

21 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_HV2RO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 86–184 Author chain B； PDBConstruct 1–99； UniProt 86–184 Author chain C； PDBConstruct 1–99； UniProt 86–184 Author chain D； PDBConstruct 1–99； UniProt 86–184

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hsh
Deposition date deposition_date	1995-03-31
Structure title title	CRYSTAL STRUCTURE AT 1.9 ANGSTROMS RESOLUTION OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) II PROTEASE COMPLEXED WITH L-735,524, AN ORALLY BIOAVAILABLE INHIBITOR OF THE HIV PROTEASES
Keywords keywords	HYDROLASE (ACID PROTEINASE), 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	28.07 Å
Radius of gyration Rg (electron density) rg_electron	27.14 Å
Forward intensity I(0) i0	28549200.00
Molecular weight molecular_weight	44033.0 kDa
Excluded volume excluded_volume	56318 Å³
Envelope volume envelope_volume	71306 Å³
Hydration-shell volume shell_volume	22316 Å³
Envelope diameter envelope_diameter	84.0 Å
Shell Rg shell_rg	33.98 Å
Envelope Rg envelope_rg	26.74 Å
Shape Rg shape_rg	27.15 Å
Total Rg total_rg	27.90 Å
Total atoms total_atoms	3106
Residues n_residues	396
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	86.2 Å
Rg (real space) rg_real	28.11 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.8550e+07
I(0) uncertainty (real space) i0_real_error	4.1000e+05
Rg (reciprocal space) rg_reciprocal	28.10 Å
I(0) (reciprocal space) i0_reciprocal	28550000.0000
Solution quality estimate total_estimate	0.8858
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.208
Kurtosis Kurtosis kurtosis	-0.870
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14780000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.873; Smooth: 0.903

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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	HIV-II PROTEASE
Molecular weight formula_weight	10728.3 kDa
EC 编号 ec_number	3.4.23.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3284

PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL

来源 Source

来源生物 organism	Human immunodeficiency virus 2
通用名 common_name	HIV-2
NCBI Class编号 ncbi_taxonomy_id	11720
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE ;
Molecular weight formula_weight	613.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1hsha_
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	d1hshb_
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	d1hshc_
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	d1hshd_
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 (4 domains)

Domain ID domain_id	1hshA00
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	1hshB00
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	1hshC00
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	1hshD00
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	56.520 Å
Unit-cell length b length_b	57.500 Å
Unit-cell length c length_c	63.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.14 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	—

fit	/app/data/saxs_computation/hs/1hsh/1hsh.fit
pddf	/app/data/pr_computation/hs/1hsh/1hsh.pr.out
profile	/app/data/saxs_computation/hs/1hsh/1hsh.dat