SAXSdb — 9mmj

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

Surface protein gp120 JR-FL V3 peptide

OrganismNot specified

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 291–333	Not recorded	19b Fab Light Chain × 1 19b Fab Heavy Chain × 1 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

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 9MMJ	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 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 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
2ESX The structure of the V3 region within gp120 of JR-FL HIV-1 strain (minimized average structure) Deposited 2005-10-27	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 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
2ESZ The structure of the V3 region within gp120 of JR-FL HIV-1 strain (ensemble) Deposited 2005-10-27	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 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 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 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 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 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

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	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–43； UniProt 291–333

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	9mmj
Deposition date deposition_date	2024-12-20
最后修订 last_revision	2026-01-21
Structure title title	Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the HIV-1 JR-FL envelope (Env) glycoprotein
Keywords keywords	19b, Fab, Fragment antigen-binding, HIV-1 Envelope, IMMUNE SYSTEM; IMMUNE SYSTEM
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	25.19 Å
Radius of gyration Rg (electron density) rg_electron	24.11 Å
Forward intensity I(0) i0	38348600.00
Molecular weight molecular_weight	47274.0 kDa
Excluded volume excluded_volume	58799 Å³
Envelope volume envelope_volume	71422 Å³
Hydration-shell volume shell_volume	24987 Å³
Envelope diameter envelope_diameter	86.2 Å
Shell Rg shell_rg	30.97 Å
Envelope Rg envelope_rg	23.97 Å
Shape Rg shape_rg	24.10 Å
Total Rg total_rg	24.92 Å
Total atoms total_atoms	3331
Residues n_residues	435
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	82.5 Å
Rg (real space) rg_real	25.18 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	3.8350e+07
I(0) uncertainty (real space) i0_real_error	5.1210e+05
Rg (reciprocal space) rg_reciprocal	25.18 Å
I(0) (reciprocal space) i0_reciprocal	38350000.0000
Solution quality estimate total_estimate	0.6943
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7409000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 0.120; Positv: 1.000; Valcen: 0.968; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	19b Fab Light Chain
Molecular weight formula_weight	23201.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3853

DIVLTQSPPSLSASVGDRVTITCQASQDISDHLSWFQQKPGKAPKLLVYGVSSLEAGVPSRFSVSGSGTHFTFTVNGLQPEDLATYFCQQYDDLPWTFGPGTVVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	19b Fab Heavy Chain
Molecular weight formula_weight	22791.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EVQLVQSGGALIQPGGSLRLSCAASGFTFVDYAMSWVRQAPGKGLQWVSTIIGSGADTYYTDSVKGRFTISRDNSNNTVHLQMNSLRADDTALYYCVRGVFDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Surface protein gp120 JR-FL V3 peptide
Molecular weight formula_weight	4919.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

EINCTRPNNNTRKSIHIGPGRWFYTTGEIIGDIRQAHCNISRA

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	478

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8. Citations (1)

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Unit-cell length a length_a	45.902 Å
Unit-cell length b length_b	87.507 Å
Unit-cell length c length_c	131.973 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	34.610 Å
R factor r_factor	0.1607
R_work r_work	0.1588
R_free r_free	0.1989

fit	/app/data/saxs_computation/mm/9mmj/9mmj.fit
pddf	/app/data/pr_computation/mm/9mmj/9mmj.pr.out
profile	/app/data/saxs_computation/mm/9mmj/9mmj.dat

Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the HIV-1 JR-FL envelope (Env) glycoprotein

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

Surface protein gp120 JR-FL V3 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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)