SAXSdb — 4fae

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

HIV-1 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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–99 Chain B； UniProt 1–99	Mutation：D25N, D35E, I36V, M46L	Substrate p2/NC peptide × 1 （Q9YP46）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；0.1 M citric acid, 2.4 M ammonium sulfate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.279

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 4FAE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3OQ7 Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants Deposited 2010-09-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa） Fragment：UNP residues 1-99	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.3-1.0M sodium chloride in the pH range 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.71 Å R-free 0.223
3OQA Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants Deposited 2010-09-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa） Fragment：UNP residues 1-99	Mutation：T82S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.3-1.0M sodium chloride in the pH range 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.25 Å R-free 0.238
3OQD Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants Deposited 2010-09-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa） Fragment：UNP residues 1-99	Mutation：T82F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.3-1.0M sodium chloride in the pH range 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.71 Å R-free 0.229
3OTY MDR769 HIV-1 protease complexed with RT/RH hepta-peptide Deposited 2010-09-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 01 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.236
3OU1 MDR769 HIV-1 protease complexed with RH/IN hepta-peptide Deposited 2010-09-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 01 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.237
3OU3 MDR769 HIV-1 protease complexed with PR/RT hepta-peptide Deposited 2010-09-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 01 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.226
3OU4 MDR769 HIV-1 protease complexed with TF/PR hepta-peptide Deposited 2010-09-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 01 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.232
3OUA MDR769 HIV-1 protease complexed with p1/p6 hepta-peptide Deposited 2010-09-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 01 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.226
3OUB MDR769 HIV-1 protease complexed with NC/p1 hepta-peptide Deposited 2010-09-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 0.1 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.236
3OUC MDR769 HIV-1 protease complexed with p2/NC hepta-peptide Deposited 2010-09-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 0.1 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.262
3OUD MDR769 HIV-1 protease complexed with CA/p2 hepta-peptide Deposited 2010-09-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 0.1 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.244
3PJ6 Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants Deposited 2010-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa） Fragment：UNP residues 1-99	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；300 K；0.3-1.0 M NaCl, pH 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.25 Å R-free 0.304
3R0W Crystal Structures of Multidrug-resistant HIV-1 Protease in Complex with Mechanism-Based Aspartyl Protease Inhibitors. Deposited 2011-03-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	RSY N-[(2R)-1-{[(2S,3S)-5-{[(2R)-1-{[(2S)-1-amino-4-methyl-1-oxopentan-2-yl]amino}-3-chloro-1-oxopropan-2-yl]amino}-3-hydroxy-5-oxo-1-phenylpentan-2-yl]amino}-3-methyl-1-oxobutan-2-yl]pyridine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；0.3 M NaCl, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.245
3R0Y Crystal Structures of Multidrug-resistant HIV-1 Protease in Complex with Mechanism-Based Aspartyl Protease Inhibitors Deposited 2011-03-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	RSZ N-[(2S)-1-{[(2S,3S)-3-hydroxy-5-oxo-5-{[(2R)-1-oxo-3-phenyl-1-(prop-2-yn-1-ylamino)propan-2-yl]amino}-1-phenylpentan-2-yl]amino}-3-methyl-1-oxobutan-2-yl]pyridine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；0.3 M NaCl, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.231
3SO9 Darunavir in Complex with a Human Immunodeficiency Virus Type 1 Protease Variant Deposited 2011-06-30	Different construct Different mutation/modification Different oligomeric state 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, UNP residues 1-99 Chain B 1–99（99 aa） Fragment：HIV-1 protease, UNP residues 1-99	Mutation：Q7K, L10I, M36V, M46L, I54V, I62V, L63P, A71V, V82T, I84V, L90M Mutation：Q7K, L10I, M36V, M46L, I54V, I62V, L63P, A71V, V82T, I84V, L90M	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 6；298 K；0.1M MES and 2.4M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.87 Å R-free 0.256
3SPK Tipranavir in Complex with a Human Immunodeficiency Virus Type 1 Protease Variant Deposited 2011-07-01	Different construct Different mutation/modification Different oligomeric state 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 Chain B 1–99（99 aa） Fragment：HIV-1 protease	Mutation：Q7K, L10I, M36V, M46L, I54V, I62V, L63P, A71V, V82T, I84V, L90M Mutation：Q7K, L10I, M36V, M46L, I54V, I62V, L63P, A71V, V82T, I84V, L90M	TPV N-(3-{(1R)-1-[(6R)-4-HYDROXY-2-OXO-6-PHENETHYL-6-PROPYL-5,6-DIHYDRO-2H-PYRAN-3-YL]PROPYL}PHENYL)-5-(TRIFLUOROMETHYL)-2-PYRIDINESULFONAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1M MES and 2.4M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.24 Å R-free 0.227
4EYR Crystal structure of multidrug-resistant clinical isolate 769 HIV-1 protease in complex with ritonavir Deposited 2012-05-01	Different construct Different mutation/modification Different oligomeric state 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：UNP residues 1-99 Chain B 1–99（99 aa） Fragment：UNP residues 1-99	Not recorded	RIT RITONAVIR × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；295 K；0.8M NaCl, 0.1 M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.80 Å R-free 0.226
4FAF Substrate CA/p2 in Complex with a Human Immunodeficiency Virus Type 1 Protease Variant Deposited 2012-05-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Mutation：D25N, D35E, I36V, M46L Mutation：D25N, D35E, I36V, M46L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1 M MES, 2.4 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.240
4L1A Crystallographic study of multi-drug resistant HIV-1 protease Lopinavir complex: mechanism of drug recognition and resistance Deposited 2013-06-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa） Chain B 1–99（99 aa）	Not recorded	AB1 N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；The hanging drop vapor diffusion method was used to form the bipyramidal crystals of the MDR 769 protease. Using a grid screen consisting of sodium chloride (0.7 to 1.4 M) and MES-HEPES buffer (pH 5.5 to 8.1), the HIV-1 protease substrate complex crystals formed overnight at 22 C. Routinely, 0.2 mm crystals, in the longest dimension, were obtained after 14 days of incubation. In each well, there were two droplets, containing 1 lL of protease substrate mixture, 1 lL of reservoir solution and 2 lL of protease substrate mixture, 1 lL of reservoir solution, respectively, 07 mL of well solution., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.260
4NKK Crystal structure of a multi-drug resistant clinical isolate-769 HIV-1 protease variant that is resistant to the dimerization inhibitory activity of TLF-PafF Deposited 2013-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.3-1.0 M NaCl (precipitant), pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.249

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q000H7_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 1–99 Author chain B； PDBConstruct 1–99； UniProt 1–99

Substrate p2/NC peptide

OrganismNot specified

UniProt Q9YP46

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 375–381	Not recorded	HIV-1 protease × 2 （Q000H7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；0.1 M citric acid, 2.4 M ammonium sulfate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.279

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 4FAE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L44 C-terminal zinc knuckle of the HIVNCp7 Deposited 2010-10-01	Different construct 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 411–429（19 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.7；298 K；Ionic strength (raw mmCIF value) 6；Pressure ambient NMR sample composition 1 mM C-terminal zinc knuckle of the HIVNCp7, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L45 C-terminal zinc knuckle of the HIVNCp7 with DNA Deposited 2010-10-01	Different construct 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 411–429（19 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.7；298 K；Ionic strength (raw mmCIF value) 6.0；Pressure ambient NMR sample composition 1 mM C-terminal zinc knuckle of the HIVNCp7, 1 mM DNA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L46 C-terminal zinc finger of the HIVNCp7 with platinated DNA Deposited 2010-10-01	Different construct 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 411–429（19 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.7；298 K；Ionic strength (raw mmCIF value) 6.0；Pressure ambient NMR sample composition 1 mM C-terminal zinc knuckle of the HIVNCp7, 1 mM DNA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3OUA MDR769 HIV-1 protease complexed with p1/p6 hepta-peptide Deposited 2010-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 446–452（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 01 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.226
3OUC MDR769 HIV-1 protease complexed with p2/NC hepta-peptide Deposited 2010-09-14	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 375–381（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 0.1 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.262
3P9G Crystal structure of the TSG101 UEV domain in complex with FA459 peptide Deposited 2010-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 453–461（9 aa） Fragment：Modified HIV-1 Gag PTAP Motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES-NAOH (PH7.5), 25% PEG 3350, 0.2M SODIUM NITRATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.242
3P9H Crystal structure of the TSG101 UEV domain in complex with FA258 peptide Deposited 2010-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 453–461（9 aa） Fragment：Modified HIV-1 Gag PTAP Motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES-NAOH (PH7.5), 25% PEG 3350, 0.2M SODIUM NITRATE , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.253
4EP3 Crystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate CA-p2 Deposited 2012-04-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 359–367（9 aa）	Not recorded	GOL GLYCEROL × 3 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.81 Å R-free 0.227
4EPJ Crystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate p2-NC Deposited 2012-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 374–381（8 aa）	Not recorded	GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 1 ACT ACETATE ION × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.69 Å R-free 0.227
4EQ0 Crystal Structure of inactive single chain variant of HIV-1 Protease in Complex with the substrate p2-NC Deposited 2012-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 374–381（8 aa）	Not recorded	BME BETA-MERCAPTOETHANOL × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 3 ACT ACETATE ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.70 Å R-free 0.264

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9YP46_9HIV1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–7； UniProt 375–381

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	4fae
Deposition date deposition_date	2012-05-22
Structure title title	Substrate p2/NC in Complex with a Human Immunodeficiency Virus Type 1 Protease Variant
Keywords keywords	protease, VIRAL PROTEIN; VIRAL PROTEIN
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	18.13 Å
Radius of gyration Rg (electron density) rg_electron	17.21 Å
Forward intensity I(0) i0	8482250.00
Molecular weight molecular_weight	22361.0 kDa
Excluded volume excluded_volume	28545 Å³
Envelope volume envelope_volume	32388 Å³
Hydration-shell volume shell_volume	16029 Å³
Envelope diameter envelope_diameter	65.0 Å
Shell Rg shell_rg	23.06 Å
Envelope Rg envelope_rg	17.70 Å
Shape Rg shape_rg	17.24 Å
Total Rg total_rg	18.14 Å
Total atoms total_atoms	1570
Residues n_residues	205
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	63.0 Å
Rg (real space) rg_real	18.13 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	8.4820e+06
I(0) uncertainty (real space) i0_real_error	1.0010e+05
Rg (reciprocal space) rg_reciprocal	18.13 Å
I(0) (reciprocal space) i0_reciprocal	8482000.0000
Solution quality estimate total_estimate	0.7708
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.4 Å
Skewness Skewness skewness	0.424
Kurtosis Kurtosis kurtosis	-0.101
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5209000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.679; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HIV-1 protease
Molecular weight formula_weight	10769.6 kDa
EC 编号 ec_number	3.4.23.16
Mutation mutation	D25N, D35E, I36V, M46L
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	1770

PQITLWQRPIVTIKIGGQLKEALLNTGADDTVLEEVNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPTNVIGRNLMTQIGCTLNF

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 polymer

Description description	Substrate p2/NC peptide
Molecular weight formula_weight	837.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

TIMMQRG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4faeA00
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	4faeB00
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	28.615 Å
Unit-cell length b length_b	63.851 Å
Unit-cell length c length_c	91.113 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2034
R_work r_work	0.2000
R_free r_free	0.2786

fit	/app/data/saxs_computation/fa/4fae/4fae.fit
pddf	/app/data/pr_computation/fa/4fae/4fae.pr.out
profile	/app/data/saxs_computation/fa/4fae/4fae.dat

Substrate p2/NC in Complex with a Human Immunodeficiency Virus Type 1 Protease Variant

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

HIV-1 protease

State in the Current Structure

Other States of the Same Protein in the Database

Substrate p2/NC peptide

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)