SAXSdb — 2esx

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

Envelope polyprotein GP160

Human immunodeficiency virus 1

UniProt P20871

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 301–319	Fragment：V3 of GP120	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5；305 K；Ionic strength (raw mmCIF value) 10mM acetic acid NMR sample composition：0.4mM V3JR-FL-447-52D complex U-15N \| 5% D2O, 95% H2O NMR sample composition：0.4mM V3JR-FL-447-52D complex U-15N-13C \| 5% D2O, 95% H2O NMR sample composition：0.4mM V3JR-FL-447-52D complex U-15N-13C \| 100% D2O	Resolution not provided

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 2ESX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CE4 CONFORMATIONAL MODEL FOR THE CONSENSUS V3 LOOP OF THE ENVELOPE PROTEIN GP120 OF HIV-1 Deposited 1999-03-15	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 294–328（35 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 2.5；290 K；Pressure 1 NMR sample composition 10% D2O/70% WATER/20% D3-TRIFLUOROETHANOL	Resolution not provided
2ESZ The structure of the V3 region within gp120 of JR-FL HIV-1 strain (ensemble) Deposited 2005-10-27	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 301–319（19 aa） Fragment：V3 of GP120	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；305 K；Ionic strength (raw mmCIF value) 10mM acetic acid NMR sample composition 0.4mM V3JR-FL-447-52D complex U-15N \| 5% D2O, 95% H2O NMR sample composition 0.4mM V3JR-FL-447-52D complex U-15N-13C \| 5% D2O, 95% H2O NMR sample composition 0.4mM V3JR-FL-447-52D complex U-15N-13C \| 100% D2O	Resolution not provided
4R2G Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 Deposited 2014-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 197–300（104 aa） Chain E 317–484（168 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.28 Å R-free 0.263
4R2G Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 Deposited 2014-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain O 197–300（104 aa） Chain O 317–484（168 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.28 Å R-free 0.263
4R2G Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 Deposited 2014-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 197–300（104 aa） Chain K 317–484（168 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.28 Å R-free 0.263
4R2G Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 Deposited 2014-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 197–300（104 aa） Chain A 317–484（168 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.28 Å R-free 0.263
9MMJ Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the HIV-1 JR-FL envelope (Env) glycoprotein Deposited 2024-12-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 291–333（43 aa）	Not recorded	ACT ACETATE ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.18 M Ammonium sulfate, 0.09 M Sodium acetate trihydrate pH 4.6, 27% w/v Polyethylene glycol monomethyl ether 2,000, 10% v/v Glycerol	Resolution 1.78 Å R-free 0.199

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ENV_HV1JR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–19； UniProt 301–319

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	2esx
Deposition date deposition_date	2005-10-27
Structure title title	The structure of the V3 region within gp120 of JR-FL HIV-1 strain (minimized average structure)
Keywords keywords	HIV-1, JR-FL, V3, 447-52D, antibody, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	10.23 Å
Radius of gyration Rg (electron density) rg_electron	9.12 Å
Forward intensity I(0) i0	142473.00
Molecular weight molecular_weight	2089.0 kDa
Excluded volume excluded_volume	2631 Å³
Envelope volume envelope_volume	3186 Å³
Hydration-shell volume shell_volume	3731 Å³
Envelope diameter envelope_diameter	34.6 Å
Shell Rg shell_rg	12.63 Å
Envelope Rg envelope_rg	9.64 Å
Shape Rg shape_rg	9.06 Å
Total Rg total_rg	10.66 Å
Total atoms total_atoms	299
Residues n_residues	19
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	37.8 Å
Rg (real space) rg_real	10.37 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.4250e+05
I(0) uncertainty (real space) i0_real_error	1.5050e+03
Rg (reciprocal space) rg_reciprocal	10.36 Å
I(0) (reciprocal space) i0_reciprocal	142500.0000
Solution quality estimate total_estimate	0.8049
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	10.5 Å
Skewness Skewness skewness	0.600
Kurtosis Kurtosis kurtosis	0.039
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18570.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.696; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.472; Smooth: 0.899

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	Envelope polyprotein GP160
Molecular weight formula_weight	2108.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	299

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

fit	/app/data/saxs_computation/es/2esx/2esx.fit
pddf	/app/data/pr_computation/es/2esx/2esx.pr.out
profile	/app/data/saxs_computation/es/2esx/2esx.dat

The structure of the V3 region within gp120 of JR-FL HIV-1 strain (minimized average structure)

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

Envelope polyprotein GP160

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)