SAXSdb — 3oz9

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

Fab NC-1 kappa light chain

OrganismNot specified

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 130–235	Not recorded	Fab NC-1 IgG2a heavy chain × 1 （P01863） GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.13M sodium citrate, 0.1M sodium borate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.233

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 3OZ9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NJ9 Crystal structure of Fab 8B10 in complex with MPTS Deposited 2013-11-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 130–236（107 aa）	Not recorded	ZN ZINC ION × 6 2M9 8-methoxypyrene-1,3,6-trisulfonic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M zinc acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 1.95 Å R-free 0.264
4NJA Crystal structure of Fab 6C8 in complex with MPTS Deposited 2013-11-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 130–236（107 aa）	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 2 2M9 8-methoxypyrene-1,3,6-trisulfonic acid × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20mM zinc acetate, 12% PEG 8000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.20 Å R-free 0.265

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q52L95_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 106–211； UniProt 130–235

Fab NC-1 IgG2a heavy chain

OrganismNot specified

UniProt P01863

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–100	Not recorded	Fab NC-1 kappa light chain × 1 （Q52L95） GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.13M sodium citrate, 0.1M sodium borate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.233

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 3OZ9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GGI CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN Deposited 1993-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–107（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1GGI CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN Deposited 1993-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–107（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1IGT STRUCTURE OF IMMUNOGLOBULIN Deposited 1996-10-25	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 B 1–326（326 aa） Chain D 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；291 K；7 MICROLITERS OF 4.3 MG/ML MAB231, 3 MICROLITERS 50 MILLIMOLAR TRIS PH 8.0, AND 7 MICROLITERS 4% PEG 3350 EQUILIBRATED AGAINST 25 ML RESERVOIRS OF 4% PEG 3350, AT 18 DEGREE CELSIUS (SANDWICH PLATE)., temperature 291K	Resolution 2.80 Å R-free 0.297
1YEC STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3) Deposited 1997-04-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.90 Å R-free 0.252
1YEC STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3) Deposited 1997-04-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.90 Å R-free 0.252
1YEF STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE ANALOGUE Deposited 1997-05-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 8 PNC PARA-NITROBENZYL GLUTARYL GLYCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.248
1YEG STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT Deposited 1997-05-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 BPN PARANITROBENZYL ALCOHOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.240
1YEG STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT Deposited 1997-05-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 BPN PARANITROBENZYL ALCOHOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.240
1YEH STRUCTURE OF IGG2A FAB FRAGMENT Deposited 1997-05-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 35% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.55 Å R-free 0.231
1YEH STRUCTURE OF IGG2A FAB FRAGMENT Deposited 1997-05-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 35% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.55 Å R-free 0.231
3ZO0 Mouse IgG2a in complex with mouse TRIM21 PRYSPRY Deposited 2013-02-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 120–327（208 aa） Fragment：FC, RESIDUES 120-327	Not recorded	MAN alpha-D-mannopyranose × 2 FUC alpha-L-fucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.99 Å R-free 0.253
5VAA Crystal structure of mouse IgG2a Fc T370K mutant Deposited 2017-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 107–330（224 aa） Fragment：UNP residues 107-330 Chain B 107–330（224 aa） Fragment：UNP residues 107-330	Mutation：T370K Mutation：T370K	GOL GLYCEROL × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；40% (w/v) PEG 200, 0.1 M MES, pH 6.5	Resolution 1.55 Å R-free 0.195
8AQW BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 98–330（233 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9RBQ Semliki Forest virus trimer 1 in complex with ApoER2 LA5 Deposited 2025-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: 13-meric	Chain A 99–330（232 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

10 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GCAA_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 120–219； UniProt 1–100

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	3oz9
Deposition date deposition_date	2010-09-24
Structure title title	Crystal Structure of anti-gp41 Fab NC-1
Keywords keywords	immunoglobulin fold, non-neutralizing antibody, HIV-1 gp41 6-helix bundle core, 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	25.08 Å
Radius of gyration Rg (electron density) rg_electron	24.11 Å
Forward intensity I(0) i0	37538600.00
Molecular weight molecular_weight	46982.0 kDa
Excluded volume excluded_volume	58490 Å³
Envelope volume envelope_volume	70662 Å³
Hydration-shell volume shell_volume	24518 Å³
Envelope diameter envelope_diameter	80.6 Å
Shell Rg shell_rg	31.12 Å
Envelope Rg envelope_rg	23.88 Å
Shape Rg shape_rg	24.10 Å
Total Rg total_rg	24.93 Å
Total atoms total_atoms	3307
Residues n_residues	424
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	78.6 Å
Rg (real space) rg_real	25.05 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	3.7540e+07
I(0) uncertainty (real space) i0_real_error	4.8460e+05
Rg (reciprocal space) rg_reciprocal	25.06 Å
I(0) (reciprocal space) i0_reciprocal	37540000.0000
Solution quality estimate total_estimate	0.9107
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.532
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8566000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Fab NC-1 kappa light chain
Molecular weight formula_weight	23102.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3833

QIVLTQSPVIMSASLGEEITLTCSASSSVSYMHWYQQKSGTSPKLLIYSTSNLASGVPSRFSGSGSGTFYSLTISSVEAEDAADYYCHQWSGFYTFGGGTKLEIQRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Entity 2 Entity 2 polymer

Description description	Fab NC-1 IgG2a heavy chain
Molecular weight formula_weight	23584.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQSGTELMKPGSSVKISCKATGYRFSSYWVEWVKQRPGHGLEWIGKILPGIGSTSYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGYYGPTWFAYWGQGTLVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	485

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3oz9h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3oz9h2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3oz9l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d3oz9l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	3oz9H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3oz9H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3oz9L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3oz9L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	41.373 Å
Unit-cell length b length_b	61.539 Å
Unit-cell length c length_c	154.373 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	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	24.380 Å
R factor r_factor	0.1922
R_work r_work	0.1900
R_free r_free	0.2330

fit	/app/data/saxs_computation/oz/3oz9/3oz9.fit
pddf	/app/data/pr_computation/oz/3oz9/3oz9.pr.out
profile	/app/data/saxs_computation/oz/3oz9/3oz9.dat

Crystal Structure of anti-gp41 Fab NC-1

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

Fab NC-1 kappa light chain

State in the Current Structure

Other States of the Same Protein in the Database

Fab NC-1 IgG2a heavy chain

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)