3ebz

High Resolution HIV-2 Protease Structure in Complex with Clinical Drug Darunavir

Method: X-RAY DIFFRACTION D_max: 61.0 Å Quality: REASONABLE

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

Protease

Human immunodeficiency virus type 2 (ISOLATE ROD)

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 514–612 Chain B； UniProt 514–612	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

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 3EBZ	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 construct 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）	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
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 Deposited 1995-03-31	Different construct 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）	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 conditions	Resolution 1.90 Å
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 Deposited 1995-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 86–184（99 aa） Chain D 86–184（99 aa）	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 conditions	Resolution 1.90 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 construct 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）	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 experimental conditions 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 construct 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）	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 construct 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）	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 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 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
3EC0 High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-06579A Deposited 2008-08-28	Different ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 38 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 514–612 Author chain B； PDBConstruct 1–99； UniProt 514–612

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	3ebz
Deposition date deposition_date	2008-08-28
Structure title title	High Resolution HIV-2 Protease Structure in Complex with Clinical Drug Darunavir
Keywords keywords	HIV-2, aspartic protease, inhibitor, protease-drug complex, 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	18.20 Å
Radius of gyration Rg (electron density) rg_electron	17.38 Å
Forward intensity I(0) i0	18479000.00
Molecular weight molecular_weight	21654.0 kDa
Excluded volume excluded_volume	20743 Å³
Envelope volume envelope_volume	32969 Å³
Hydration-shell volume shell_volume	16188 Å³
Envelope diameter envelope_diameter	61.3 Å
Shell Rg shell_rg	23.09 Å
Envelope Rg envelope_rg	17.73 Å
Shape Rg shape_rg	17.31 Å
Total Rg total_rg	18.17 Å
Total atoms total_atoms	1596
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	61.0 Å
Rg (real space) rg_real	18.18 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.8480e+07
I(0) uncertainty (real space) i0_real_error	2.1520e+05
Rg (reciprocal space) rg_reciprocal	18.18 Å
I(0) (reciprocal space) i0_reciprocal	18480000.0000
Solution quality estimate total_estimate	0.7197
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.366
Kurtosis Kurtosis kurtosis	-0.230
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4535000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 0.330; Positv: 1.000; Valcen: 0.996; Smooth: 0.953

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Protease
Molecular weight formula_weight	10728.3 kDa
EC 编号 ec_number	3.4.23.47
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	1861

PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL

来源 Source

来源生物 organism	Human immunodeficiency virus type 2 (ISOLATE ROD)
NCBI Class编号 ncbi_taxonomy_id	11720
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
Molecular weight formula_weight	547.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	210

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ebza_
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	d3ebzb_
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	3ebzA00
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	3ebzB00
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	105.408 Å
Unit-cell length b length_b	30.827 Å
Unit-cell length c length_c	55.768 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1359
R_work r_work	0.1245
R_free r_free	0.1812

fit	/app/data/saxs_computation/eb/3ebz/3ebz.fit
pddf	/app/data/pr_computation/eb/3ebz/3ebz.pr.out
profile	/app/data/saxs_computation/eb/3ebz/3ebz.dat