3dph

HIV-1 capsid C-terminal domain mutant (L211S)

Method: X-RAY DIFFRACTION D_max: 63.6 Å Quality: GOOD

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

HIV-1 CAPSID PROTEIN

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 278–363 Chain B； UniProt 278–363	Fragment：C-terminal domain, UNP residues 278 to 363 Mutation：L211S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7.5；292 K；30% PEG4000, 100mM NaHEPES, 200mM CaCl2, pH 7.5, EVAPORATION, temperature 292K	Resolution 2.01 Å R-free 0.254

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 3DPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L6N STRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE HIV-1 GAG POLYPROTEIN Deposited 2002-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–283（283 aa） Fragment：Residues 1-283	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 1mM U-15N,13C gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME \| 95% H2O/5% D2O NMR sample composition 1mM U-15N,13C gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME \| 100% D2O NMR sample composition 1mM U-15N,2H gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME \| 95% H2O/5% D2O NMR sample composition 1mM U-15N gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME \| 95% H2O/5% D2O	Resolution not provided
1M9C X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type Complex. Deposited 2002-07-28	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 D 133–278（146 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.00 Å R-free 0.259
1M9C X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type Complex. Deposited 2002-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 133–278（146 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.00 Å R-free 0.259
1M9D X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) O-type chimera Complex. Deposited 2002-07-28	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 D 133–278（146 aa） Fragment：N-TERMINAL DOMAIN	Mutation：L83T, V86P, H87A, A88M, I91L, A92P, M96I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.90 Å R-free 0.232
1M9D X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) O-type chimera Complex. Deposited 2002-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 133–278（146 aa） Fragment：N-TERMINAL DOMAIN	Mutation：L83T, V86P, H87A, A88M, I91L, A92P, M96I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.90 Å R-free 0.232
1M9E X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex. Deposited 2002-07-28	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 D 133–278（146 aa） Fragment：N-terminal domain	Mutation：H87A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.72 Å R-free 0.226
1M9E X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex. Deposited 2002-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 133–278（146 aa） Fragment：N-terminal domain	Mutation：H87A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.72 Å R-free 0.226
1M9F X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M Complex. Deposited 2002-07-28	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 D 133–278（146 aa） Fragment：N-terminal domain	Mutation：H87A,A88M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.73 Å R-free 0.220
1M9F X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M Complex. Deposited 2002-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 133–278（146 aa） Fragment：N-terminal domain	Mutation：H87A,A88M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.73 Å R-free 0.220
1M9X X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M,G89A Complex. Deposited 2002-07-30	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 D 133–278（146 aa） Fragment：N-TERMINAL DOMAIN	Mutation：H87A,A88M,G89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.70 Å R-free 0.230
1M9X X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M,G89A Complex. Deposited 2002-07-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 133–278（146 aa） Fragment：N-TERMINAL DOMAIN	Mutation：H87A,A88M,G89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.70 Å R-free 0.230
1M9X X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M,G89A Complex. Deposited 2002-07-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 133–278（146 aa） Fragment：N-TERMINAL DOMAIN	Mutation：H87A,A88M,G89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.70 Å R-free 0.230
1M9X X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M,G89A Complex. Deposited 2002-07-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 133–278（146 aa） Fragment：N-TERMINAL DOMAIN	Mutation：H87A,A88M,G89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.70 Å R-free 0.230
1M9Y X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex. Deposited 2002-07-30	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 D 133–278（146 aa） Fragment：N-terminal domain	Mutation：H87A,G89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.90 Å R-free 0.234
1M9Y X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex. Deposited 2002-07-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 133–278（146 aa） Fragment：N-terminal domain	Mutation：H87A,G89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.90 Å R-free 0.234
1M9Y X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex. Deposited 2002-07-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 133–278（146 aa） Fragment：N-terminal domain	Mutation：H87A,G89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.90 Å R-free 0.234
1M9Y X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex. Deposited 2002-07-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 133–278（146 aa） Fragment：N-terminal domain	Mutation：H87A,G89A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.90 Å R-free 0.234
2BUO HIV-1 capsid C-terminal domain in complex with an inhibitor of particle assembly Deposited 2005-06-17	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 A 278–363（86 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 278-363	Not recorded	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 32% PEG 4000 100MM AMMONIUM SULFATE PH4.6 10MM MGCL2	Resolution 1.70 Å R-free 0.234
2JMG Solution structure of V7R mutant of HIV-1 myristoylated matrix protein Deposited 2006-11-11	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 2–132（131 aa） Fragment：MATRIX DOMAIN, RESIDUES 2-132	Mutation：V7R	MYR MYRISTIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 5.5；308 K；Pressure ambient NMR sample composition 1 mM [U-100% 13C, U-100% 15N] HIV-1 V7R-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] HIV-1 V7R-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM HIV-1 V7R-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LF4 Structure of a monomeric mutant of the HIV-1 capsid protein Deposited 2011-06-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 133–363（231 aa）	Mutation：W184A, M185A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；303 K；Pressure ambient NMR sample composition 2 mM [U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 100% D2O \| 100% D2O NMR sample composition 2 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 100% D2O \| 100% D2O NMR sample composition 2 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 100% D2O \| 100% D2O	Resolution not provided
2NV3 Solution structure of L8A mutant of HIV-1 myristoylated matrix protein Deposited 2006-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–132（131 aa） Fragment：matrix domain, residues 2-132	Mutation：L8A	MYR MYRISTIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 5.5；308 K；Pressure ambient NMR sample composition 1 mM [U-100% 13C, U-100% 15N] HIV-1 L8A-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] HIV-1 L8A-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM HIV-1 L8A-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3DS0 HIV-1 capsid C-terminal domain mutant (N183A) in complex with an inhibitor of particle assembly (CAI) Deposited 2008-07-11	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 A 278–363（86 aa） Fragment：C-terminal domain, residues 278-363	Mutation：N183A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.2；298 K；32% PEG 4000, 100mM ammonium acetate pH4.2, 10mM MgCl2, EVAPORATION, temperature 298.0K	Resolution 1.60 Å R-free 0.245
3DS0 HIV-1 capsid C-terminal domain mutant (N183A) in complex with an inhibitor of particle assembly (CAI) Deposited 2008-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 278–363（86 aa） Fragment：C-terminal domain, residues 278-363	Mutation：N183A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.2；298 K；32% PEG 4000, 100mM ammonium acetate pH4.2, 10mM MgCl2, EVAPORATION, temperature 298.0K	Resolution 1.60 Å R-free 0.245
3DS1 HIV-1 capsid C-terminal domain mutant (E187A) in complex with an inhibitor of particle assembly (CAI) Deposited 2008-07-11	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 A 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：E187A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.2；298 K；30% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.2, EVAPORATION, temperature 298.0K	Resolution 1.60 Å R-free 0.272
3DS1 HIV-1 capsid C-terminal domain mutant (E187A) in complex with an inhibitor of particle assembly (CAI) Deposited 2008-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：E187A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.2；298 K；30% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.2, EVAPORATION, temperature 298.0K	Resolution 1.60 Å R-free 0.272
3DS2 HIV-1 capsid C-terminal domain mutant (Y169A) Deposited 2008-07-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363 Chain B 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：Y169A Mutation：Y169A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；298 K；20% PEG 3350, 200mM sodium iodide, pH 7.5, EVAPORATION, temperature 298.0K	Resolution 1.20 Å R-free 0.246
3DS3 HIV-1 capsid C-terminal domain mutant (Y169A) in complex with an inhibitor of particle assembly (CAI) Deposited 2008-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363 Chain B 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：Y169A Mutation：Y169A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；298 K；30% PEG4000, 200mM ammonium acetate, 100mm sodium acetate pH 4.6, EVAPORATION, temperature 298K	Resolution 2.70 Å R-free 0.293
3DS4 HIV-1 capsid C-terminal domain mutant (L211S) in complex with an inhibitor of particle assembly (CAI) Deposited 2008-07-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363 Chain B 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：L211S Mutation：L211S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；298 K；PEG4000, 200mM ammonium sulfate, EVAPORATION, temperature 298K	Resolution 1.12 Å R-free 0.234
3DS5 HIV-1 capsid C-terminal domain mutant (N183A) Deposited 2008-07-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363 Chain D 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：N183A Mutation：N183A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；298 K；30% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.6, EVAPORATION, temperature 298.0K	Resolution 2.40 Å R-free 0.270
3DS5 HIV-1 capsid C-terminal domain mutant (N183A) Deposited 2008-07-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363 Chain B 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：N183A Mutation：N183A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；298 K；30% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.6, EVAPORATION, temperature 298.0K	Resolution 2.40 Å R-free 0.270
3DTJ HIV-1 capsid C-terminal domain mutant (E187A) Deposited 2008-07-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363 Chain D 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：E187A Mutation：E187A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；298 K；32% PEG 4,000, 100 mM ammonium acetate pH 5.0 and 10 mM MgCl2., EVAPORATION, temperature 298K	Resolution 4.00 Å
3DTJ HIV-1 capsid C-terminal domain mutant (E187A) Deposited 2008-07-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363 Chain B 278–363（86 aa） Fragment：C-terminal domain, UNP residues 278-363	Mutation：E187A Mutation：E187A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；298 K；32% PEG 4,000, 100 mM ammonium acetate pH 5.0 and 10 mM MgCl2., EVAPORATION, temperature 298K	Resolution 4.00 Å
3OBU Crystal structure of the Tsg101 UEV domain in complex with a HIV-1 PTAP peptide Deposited 2010-08-09	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：HIV-1 Gag PTAP motif (5-13)	Not recorded	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 1.60 Å R-free 0.236
3OBX Crystal structure of the Tsg101 UEV domain in complex with a HIV-1 Gag P7A mutant peptide Deposited 2010-08-09	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：HIV-1 Gag PTAP motif (5-13)	Mutation：P7A mutant	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 1.60 Å R-free 0.230
3P05 X-ray structure of pentameric HIV-1 CA Deposited 2010-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 133–363（231 aa） Fragment：UNP residues 133-363 Chain B 133–363（231 aa） Fragment：UNP residues 133-363 Chain C 133–363（231 aa） Fragment：UNP residues 133-363 Chain D 133–363（231 aa） Fragment：UNP residues 133-363 Chain E 133–363（231 aa） Fragment：UNP residues 133-363	Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A Mutation：N21C, A22C, W184A, M185A	IOD IODIDE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27-30% PEG 4000, 100 mM Tris, 0.2 M sodium iodide, pH 8-9, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.266
3P0A X-ray structure of pentameric HIV-1 CA Deposited 2010-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 133–363（231 aa） Fragment：UNP residues 133-363 Chain B 133–363（231 aa） Fragment：UNP residues 133-363 Chain C 133–363（231 aa） Fragment：UNP residues 133-363 Chain D 133–363（231 aa） Fragment：UNP residues 133-363 Chain E 133–363（231 aa） Fragment：UNP residues 133-363	Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30-32% PEG 2000 MME, 100 mM Tris, 0.4 M sodium iodide, pH 7-8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 5.95 Å R-free 0.316
3P0A X-ray structure of pentameric HIV-1 CA Deposited 2010-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 133–363（231 aa） Fragment：UNP residues 133-363 Chain G 133–363（231 aa） Fragment：UNP residues 133-363 Chain H 133–363（231 aa） Fragment：UNP residues 133-363 Chain I 133–363（231 aa） Fragment：UNP residues 133-363 Chain J 133–363（231 aa） Fragment：UNP residues 133-363	Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30-32% PEG 2000 MME, 100 mM Tris, 0.4 M sodium iodide, pH 7-8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 5.95 Å R-free 0.316
3P0A X-ray structure of pentameric HIV-1 CA Deposited 2010-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain K 133–363（231 aa） Fragment：UNP residues 133-363 Chain L 133–363（231 aa） Fragment：UNP residues 133-363 Chain M 133–363（231 aa） Fragment：UNP residues 133-363 Chain N 133–363（231 aa） Fragment：UNP residues 133-363 Chain O 133–363（231 aa） Fragment：UNP residues 133-363	Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30-32% PEG 2000 MME, 100 mM Tris, 0.4 M sodium iodide, pH 7-8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 5.95 Å R-free 0.316
3P0A X-ray structure of pentameric HIV-1 CA Deposited 2010-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain P 133–363（231 aa） Fragment：UNP residues 133-363 Chain Q 133–363（231 aa） Fragment：UNP residues 133-363 Chain R 133–363（231 aa） Fragment：UNP residues 133-363 Chain S 133–363（231 aa） Fragment：UNP residues 133-363 Chain T 133–363（231 aa） Fragment：UNP residues 133-363	Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A Mutation：P17C, R18L, T19C, W184A, M185A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30-32% PEG 2000 MME, 100 mM Tris, 0.4 M sodium iodide, pH 7-8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 5.95 Å R-free 0.316
4DGA TRIMCyp cyclophilin domain from Macaca mulatta: HIV-1 CA(O-loop) complex Deposited 2012-01-25	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 C 133–277（145 aa） Fragment：cyclophilin-binding domain (UNP residues 133-277)	Mutation：yes	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；20% w/v PEG5000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 1.90 Å R-free 0.243
4DGA TRIMCyp cyclophilin domain from Macaca mulatta: HIV-1 CA(O-loop) complex Deposited 2012-01-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 133–277（145 aa） Fragment：cyclophilin-binding domain (UNP residues 133-277)	Mutation：yes	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；20% w/v PEG5000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 1.90 Å R-free 0.243
4DGE TRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant, HIV-1 CA(O-loop) complex Deposited 2012-01-25	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 C 133–277（145 aa） Fragment：cyclophilin-binding domain (UNP residues 133-277)	Mutation：yes	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；290 K；23.5% w/v PEG8000, 0.1 M HEPES, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.20 Å R-free 0.255
4DGE TRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant, HIV-1 CA(O-loop) complex Deposited 2012-01-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 133–277（145 aa） Fragment：cyclophilin-binding domain (UNP residues 133-277)	Mutation：yes	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；290 K；23.5% w/v PEG8000, 0.1 M HEPES, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.20 Å R-free 0.255
7R7P Immature HIV-1 CACTD-SP1 lattice with Bevirimat (BVM) and Inositol hexakisphosphate (IP6) Deposited 2021-06-25	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 × 6 PDB declaration: hexameric	Chain G 278–377（100 aa） Chain H 278–377（100 aa） Chain I 278–377（100 aa） Chain J 278–377（100 aa） Chain K 278–377（100 aa） Chain L 278–377（100 aa）	Mutation：P241T Mutation：P241T Mutation：P241T Mutation：P241T Mutation：P241T Mutation：P241T	IHP INOSITOL HEXAKISPHOSPHATE × 1 2I4 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid × 1	SOLID-STATE NMR NMR measurement conditions pH 8；277.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR measurement conditions pH 8；263.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR measurement conditions pH 8；277.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR measurement conditions pH 8；268.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR sample composition 400 uM [U-100% 13C; U-100% 15N] HIV-1 CACTD-SP1, 400 uM IP6, 360 uM BVM, Protein buffer \| Protein buffer NMR sample composition 400 uM [U-100% 13C; U-100% 15N; 99.9%-2H] HIV-1 CACTD-SP1, 400 uM IP6, 360 uM Bevirimat, protein buffer \| protein buffer	Resolution not provided
7R7Q Immature HIV-1 CACTD-SP1 lattice with Inositol hexakisphosphate (IP6) Deposited 2021-06-25	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 × 6 PDB declaration: hexameric	Chain G 278–377（100 aa） Chain H 278–377（100 aa） Chain I 278–377（100 aa） Chain J 278–377（100 aa） Chain K 278–377（100 aa） Chain L 278–377（100 aa）	Mutation：P241T Mutation：P241T Mutation：P241T Mutation：P241T Mutation：P241T Mutation：P241T	IHP INOSITOL HEXAKISPHOSPHATE × 1	SOLID-STATE NMR NMR measurement conditions pH 8；277.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR measurement conditions pH 8；263.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR measurement conditions pH 8；194.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR measurement conditions pH 8；277.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR measurement conditions pH 8；268.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR measurement conditions pH 8；277.15 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR sample composition 400 uM [U-100% 13C; U-100% 15N] HIV-1 CACTD-SP1, 400 uM IP6, Protein buffer \| Protein buffer NMR sample composition 400 uM [U-100% 13C; U-100% 15N; 99.9%-2H] HIV-1 CACTD-SP1, 400 uM IP6, Protein buffer \| Protein buffer NMR sample composition 400 uM [U-100% 13C; U-100% 15N; 99.9%-2H] HIV-1 CACTD-SP1, 400 uM IP6 S2, Protein buffer \| Protein buffer	Resolution not provided
9RMX CryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm) Deposited 2025-06-19	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 × 44 PDB declaration: 44-meric	Chain U 133–363（231 aa） Chain V 133–363（231 aa） Chain W 133–363（231 aa） Chain X 133–363（231 aa） Chain Y 133–363（231 aa） Chain Z 133–363（231 aa） Chain a 133–363（231 aa） Chain b 133–363（231 aa） Chain c 133–363（231 aa） Chain d 133–363（231 aa） Chain e 133–363（231 aa） Chain f 133–363（231 aa） Chain g 133–363（231 aa） Chain h 133–363（231 aa） Chain i 133–363（231 aa） Chain j 133–363（231 aa） Chain k 133–363（231 aa） Chain l 133–363（231 aa） Chain m 133–363（231 aa） Chain n 133–363（231 aa） Chain o 133–363（231 aa） Chain p 133–363（231 aa） Chain q 133–363（231 aa） Chain r 133–363（231 aa） Chain s 133–363（231 aa） Chain t 133–363（231 aa） Chain u 133–363（231 aa） Chain v 133–363（231 aa） Chain w 133–363（231 aa） Chain x 133–363（231 aa） Chain y 133–363（231 aa） Chain z 133–363（231 aa）	Not recorded	ZN ZINC ION × 12 IHP INOSITOL HEXAKISPHOSPHATE × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.63 Å

27 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q72497_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–86； UniProt 278–363 Author chain B； PDBConstruct 1–86； UniProt 278–363

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	3dph
Deposition date deposition_date	2008-07-08
Structure title title	HIV-1 capsid C-terminal domain mutant (L211S)
Keywords keywords	HIV, CAPSID, MUTANT, ASSEMBLY, POLYPROTEIN, VIRAL PROTEIN, Mainly Alpha, Capsid maturation, Capsid 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	18.77 Å
Radius of gyration Rg (electron density) rg_electron	17.90 Å
Forward intensity I(0) i0	6042860.00
Molecular weight molecular_weight	17418.0 kDa
Excluded volume excluded_volume	21608 Å³
Envelope volume envelope_volume	26098 Å³
Hydration-shell volume shell_volume	13026 Å³
Envelope diameter envelope_diameter	63.2 Å
Shell Rg shell_rg	22.71 Å
Envelope Rg envelope_rg	18.10 Å
Shape Rg shape_rg	17.89 Å
Total Rg total_rg	18.75 Å
Total atoms total_atoms	1218
Residues n_residues	158
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	63.6 Å
Rg (real space) rg_real	18.84 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	6.0430e+06
I(0) uncertainty (real space) i0_real_error	8.7440e+04
Rg (reciprocal space) rg_reciprocal	18.84 Å
I(0) (reciprocal space) i0_reciprocal	6043000.0000
Solution quality estimate total_estimate	0.8554
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.6 Å
Skewness Skewness skewness	0.392
Kurtosis Kurtosis kurtosis	-0.438
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2442000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.761; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3dpha_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.3 — Retrovirus capsid dimerization domain-like
Family Family family	a.28.3.1 — Retrovirus capsid protein C-terminal domain

Domain ID domain_id	d3dphb_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.3 — Retrovirus capsid dimerization domain-like
Family Family family	a.28.3.1 — Retrovirus capsid protein C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	3dphA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	30 — Retrovirus capsid C-terminal domain

Domain ID domain_id	3dphB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	30 — Retrovirus capsid C-terminal domain

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8. Citations (2)

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Unit-cell length a length_a	29.839 Å
Unit-cell length b length_b	74.909 Å
Unit-cell length c length_c	32.708 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	37.450 Å
R factor r_factor	0.1910
R_work r_work	0.1878
R_free r_free	0.2539

Description description	HIV-1 CAPSID PROTEIN
Molecular weight formula_weight	9504.8 kDa
Mutation mutation	L211S
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1325

HIV-1 capsid C-terminal domain mutant (L211S)

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

HIV-1 CAPSID PROTEIN

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Human immunodeficiency virus 1
通用名 common_name	HIV-1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

fit	/app/data/saxs_computation/dp/3dph/3dph.fit
pddf	/app/data/pr_computation/dp/3dph/3dph.pr.out
profile	/app/data/saxs_computation/dp/3dph/3dph.dat