SAXSdb — 3th9

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

Gag-Pol polyprotein

Human immunodeficiency virus type 1 lw12.3 isolate

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 489–587 Chain B； UniProt 489–587	Fragment：HIV protease Mutation：Q7K V32I L63I	9Y9 tert-butyl {(2S,3R)-4-[(4S)-7-fluoro-4-methyl-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；0.1 M sodium acetate buffer, 0.4M NaCl, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.34 Å R-free 0.190

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 3TH9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LP3 p15 HIV RNaseH domain with inhibitor MK3 Deposited 2010-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1014–1149（136 aa） Fragment：residues 1014-1149	Not recorded	MN MANGANESE (II) ION × 2 LP9 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6.8；298 K；0.1 M Sodium citrate pH 5.0, 15-20% PEG 8000, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.288
3LP3 p15 HIV RNaseH domain with inhibitor MK3 Deposited 2010-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1014–1149（136 aa） Fragment：residues 1014-1149	Not recorded	MN MANGANESE (II) ION × 2 LP9 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6.8；298 K；0.1 M Sodium citrate pH 5.0, 15-20% PEG 8000, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.288
3LP3 p15 HIV RNaseH domain with inhibitor MK3 Deposited 2010-02-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1014–1149（136 aa） Fragment：residues 1014-1149 Chain B 1014–1149（136 aa） Fragment：residues 1014-1149	Not recorded	MN MANGANESE (II) ION × 4 LP9 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6.8；298 K；0.1 M Sodium citrate pH 5.0, 15-20% PEG 8000, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.288
3VFA Crystal Structure of HIV-1 Protease Mutant V82A with novel P1'-Ligands GRL-02031 Deposited 2012-01-09	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 489–587（99 aa） Fragment：UNP residues 501-599 Chain B 489–587（99 aa） Fragment：UNP residues 501-599	Mutation：Q507K, L33I5, L563I, C567A, V582A, C595A Mutation：Q507K, L33I5, L563I, C567A, V582A, C595A	031 (3aS,5R,6aR)-hexahydro-2H-cyclopenta[b]furan-5-yl [(1S,2R)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2R)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；0.6M NaCl, 0.1M Sodium Acetate buffer pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.218
4I8W Crystal structure of wild type HIV-1 protease in complex with non-peptidic inhibitor, GRL007 Deposited 2012-12-04	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 489–587（99 aa） Chain B 489–587（99 aa）	Not recorded	G07 4-{[(2R,3S)-3-({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yloxy]carbonyl}amino)-2-hydroxy-4-phenylbutyl](2-methylpropyl)sulfamoyl}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；1.6 M ammonium sulfate (precipitant) in 0.1 M BICINE buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.96 Å R-free 0.233
4I8Z Crystal structure of wild type HIV-1 protease in complex with non-peptidic inhibitor, GRL008 Deposited 2012-12-04	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 489–587（99 aa） Chain B 489–587（99 aa）	Not recorded	G08 (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[(4-carbamoylphenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；1.6 M ammonium sulfate (precipitant) in 0.1 M BICINE buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.220
4MC1 HIV protease in complex with SA526P Deposited 2013-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 489-587 Chain B 489–587（99 aa） Fragment：UNP residues 489-587	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	CL CHLORIDE ION × 3 526 (3S)-tetrahydrofuran-3-yl {(2S,3R)-4-[(4S)-4-tert-butyl-7-fluoro-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.39 Å R-free 0.188
4MC2 HIV protease in complex with SA525P Deposited 2013-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 489-587 Chain B 489–587（99 aa） Fragment：UNP residues 489-587	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	525 (3S)-tetrahydrofuran-3-yl {(2S,3R)-4-[(4R)-4-tert-butyl-7-fluoro-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.56 Å R-free 0.207
4MC6 HIV protease in complex with SA499 Deposited 2013-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 489-587 Chain B 489–587（99 aa） Fragment：UNP residues 489-587	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	23K 1-tert-butyl-3-{(2S,3R)-4-[(4R)-7-fluoro-1,1-dioxido-4-(propan-2-yl)-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}urea × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.31 Å R-free 0.198
4MC9 HIV protease in complex with AA74 Deposited 2013-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：UNP residues 489-587 Chain B 489–587（99 aa） Fragment：UNP residues 489-587	Mutation：Q7K V32I L63I Mutation：Q7K V32I L63I	23L (3S)-tetrahydrofuran-3-yl {(2S,3R)-4-[(4R)-7-fluoro-1,1-dioxido-4-(propan-2-yl)-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate × 2 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.19 Å R-free 0.195
4NYF HIV integrase in complex with inhibitor Deposited 2013-12-10	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 1199–1357（159 aa） Fragment：Integrase catalytic domain residues 1199-1357 Chain B 1199–1357（159 aa） Fragment：Integrase catalytic domain residues 1199-1357	Mutation：C56S, W131D, F139D, F185K Mutation：C56S, W131D, F139D, F185K	4BI (2S)-tert-butoxy[4-(4-chlorophenyl)-2-methylquinolin-3-yl]ethanoic acid × 1 CD CADMIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；297 K；1.2 -1.5 M Ammonium Sulfate, 100mM Na citrate pH 5.6, 50mM Cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.90 Å R-free 0.223
4QGI X-ray crystal structure of HIV-1 protease variant G48T/L89M in complex with Saquinavir Deposited 2014-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 489–587（99 aa） Fragment：HIV-1 Protease Chain A, unp residues 489-587 Chain B 489–587（99 aa） Fragment：HIV-1 Protease Chain A, unp residues 489-587	Mutation：G48T, L89M Mutation：G48T, L89M	ROC (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M Sodium citrate, 20% 2-propanol, 20% PEG 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.246
5K14 HIV-1 Reverse Transcriptase in complex with a 2,6-difluorophenyl DAPY analog Deposited 2016-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 588–1027（440 aa）	Not recorded	IB1 4-{[4-(2,6-difluoro-4-methoxybenzene-1-carbonyl)pyrimidin-2-yl]amino}benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.0M K/Na tartrate 100mM MES pH 6.0	Resolution 2.40 Å R-free 0.261
6Y9V Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-8,13) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.90 Å
6Y9W Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,8) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6Y9X Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,7) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
6Y9Y Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-7,13) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
6Y9Z Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,9) Deposited 2020-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 133–352（220 aa） Chain B 133–352（220 aa） Chain C 133–352（220 aa） Chain D 133–352（220 aa） Chain G 133–352（220 aa） Chain H 133–352（220 aa） Chain N 133–352（220 aa） Chain Y 133–352（220 aa） Chain d 133–352（220 aa） Chain e 133–352（220 aa） Chain j 133–352（220 aa） Chain k 133–352（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
9JA0 The capsid protein of HIV 1 Deposited 2024-08-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 133–353（221 aa） Chain B 133–353（221 aa） Chain C 133–353（221 aa） Chain D 133–353（221 aa） Chain E 133–353（221 aa） Chain F 133–353（221 aa） Chain G 133–353（221 aa） Chain H 133–353（221 aa） Chain I 133–353（221 aa） Chain J 133–353（221 aa） Chain K 133–353（221 aa） Chain L 133–353（221 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

17 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_HV1LW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 489–587 Author chain B； PDBConstruct 1–99； UniProt 489–587

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	3th9
Deposition date deposition_date	2011-08-18
Structure title title	Crystal Structure of HIV-1 Protease Mutant Q7K V32I L63I with a cyclic sulfonamide inhibitor
Keywords keywords	enzyme inhibition, aspartic protease, HIV/AIDS, conformational change, Amprenavir, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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	18.02 Å
Radius of gyration Rg (electron density) rg_electron	17.04 Å
Forward intensity I(0) i0	7729350.00
Molecular weight molecular_weight	21862.0 kDa
Excluded volume excluded_volume	28086 Å³
Envelope volume envelope_volume	31310 Å³
Hydration-shell volume shell_volume	15686 Å³
Envelope diameter envelope_diameter	59.4 Å
Shell Rg shell_rg	22.76 Å
Envelope Rg envelope_rg	17.40 Å
Shape Rg shape_rg	17.05 Å
Total Rg total_rg	18.01 Å
Total atoms total_atoms	1535
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	60.5 Å
Rg (real space) rg_real	17.99 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	7.7290e+06
I(0) uncertainty (real space) i0_real_error	9.2030e+04
Rg (reciprocal space) rg_reciprocal	18.00 Å
I(0) (reciprocal space) i0_reciprocal	7729000.0000
Solution quality estimate total_estimate	0.7895
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.342
Kurtosis Kurtosis kurtosis	-0.276
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3358000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; 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	Gag-Pol polyprotein
Molecular weight formula_weight	10804.8 kDa
EC 编号 ec_number	3.4.23.16
Mutation mutation	Q7K V32I L63I
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	1813

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

来源 Source

来源生物 organism	Human immunodeficiency virus type 1 lw12.3 isolate
通用名 common_name	HIV-1
NCBI Class编号 ncbi_taxonomy_id	82834
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;tert-butyl {(2S,3R)-4-[(4S)-7-fluoro-4-methyl-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate ;
Molecular weight formula_weight	492.6 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	238

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3th9a_
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	d3th9b_
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	3th9A00
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	3th9B00
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	58.680 Å
Unit-cell length b length_b	85.890 Å
Unit-cell length c length_c	46.270 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.340 Å
Low-resolution limit resolution_low	48.450 Å
R factor r_factor	0.1812
R_work r_work	0.1810
R_free r_free	0.1904

fit	/app/data/saxs_computation/th/3th9/3th9.fit
pddf	/app/data/pr_computation/th/3th9/3th9.pr.out
profile	/app/data/saxs_computation/th/3th9/3th9.dat

Crystal Structure of HIV-1 Protease Mutant Q7K V32I L63I with a cyclic sulfonamide inhibitor

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

Gag-Pol polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction