SAXSdb — 1n4x

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

immunoglobulin kappa chain variable region

Mus musculus

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 23–130	Not recorded	immunoglobulin heavy chain variable region × 1 （Q921A6） CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.70 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 23–130	Not recorded	immunoglobulin heavy chain variable region × 1 （Q921A6） CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.70 Å R-free 0.256

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 1N4X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I9I NATIVE CRYSTAL STRUCTURE OF THE RECOMBINANT MONOCLONAL WILD TYPE ANTI-TESTOSTERONE FAB FRAGMENT Deposited 2001-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；peg3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.72 Å R-free 0.252
1I9J TESTOSTERONE COMPLEX STRUCTURE OF THE RECOMBINANT MONOCLONAL WILD TYPE ANTI-TESTOSTERONE FAB FRAGMENT Deposited 2001-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa）	Not recorded	TES TESTOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；peg3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.255
1L7T Crystal Structure Analysis of the anti-testosterone Fab fragment Deposited 2002-03-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa） Fragment：fab77 fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；peg3350, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.275
1LO2 Retro-Diels-Alderase Catalytic Antibody Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 20–238（219 aa） Fragment：Fab fragment	Not recorded	OX1 [2'-CARBOXYLETHYL]-10-METHYL-ANTHRACENE ENDOPEROXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；290 K；PEG3350, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.248
1LO2 Retro-Diels-Alderase Catalytic Antibody Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa） Fragment：Fab fragment	Not recorded	OX1 [2'-CARBOXYLETHYL]-10-METHYL-ANTHRACENE ENDOPEROXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；290 K；PEG3350, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.248
1LO3 Retro-Diels-Alderase Catalytic Antibody: Product Analogue Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 20–238（219 aa） Fragment：Fab fragment	Not recorded	AN1 3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；PEG3350, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.259
1LO3 Retro-Diels-Alderase Catalytic Antibody: Product Analogue Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa） Fragment：Fab fragment	Not recorded	AN1 3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；PEG3350, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.259
1LO4 Retro-Diels-Alderase Catalytic antibody 9D9 Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 24–236（213 aa） Fragment：Fab fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；PEG4000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.40 Å R-free 0.308

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q99M37
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 2–111； UniProt 23–130 Author chain M； PDBConstruct 2–111； UniProt 23–130

immunoglobulin heavy chain variable region

Mus musculus

UniProt Q921A6

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 2–117	Not recorded	immunoglobulin kappa chain variable region × 1 （Q99M37） CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.70 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 2–117	Not recorded	immunoglobulin kappa chain variable region × 1 （Q99M37） CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.70 Å R-free 0.256

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 1N4X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZEA Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide Deposited 2005-04-18	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 6–118（113 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；PEG 8000, citrat buffer, potassium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.78 Å R-free 0.248

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q921A6_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 4–117； UniProt 2–117 Author chain I； PDBConstruct 4–117； UniProt 2–117

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	1n4x
Deposition date deposition_date	2002-11-02
Structure title title	Structure of scFv 1696 at acidic pH
Keywords keywords	immunoglobulin, 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	29.52 Å
Radius of gyration Rg (electron density) rg_electron	29.17 Å
Forward intensity I(0) i0	44266100.00
Molecular weight molecular_weight	51833.0 kDa
Excluded volume excluded_volume	64564 Å³
Envelope volume envelope_volume	80607 Å³
Hydration-shell volume shell_volume	24100 Å³
Envelope diameter envelope_diameter	101.8 Å
Shell Rg shell_rg	34.59 Å
Envelope Rg envelope_rg	28.97 Å
Shape Rg shape_rg	29.13 Å
Total Rg total_rg	29.81 Å
Total atoms total_atoms	3658
Residues n_residues	465
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	97.8 Å
Rg (real space) rg_real	29.74 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	4.4270e+07
I(0) uncertainty (real space) i0_real_error	6.7360e+05
Rg (reciprocal space) rg_reciprocal	29.65 Å
I(0) (reciprocal space) i0_reciprocal	44260000.0000
Solution quality estimate total_estimate	0.6279
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.442
Kurtosis Kurtosis kurtosis	-0.604
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7027000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 0.092; Positv: 1.000; Valcen: 0.769; Smooth: 0.840

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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	immunoglobulin kappa chain variable region
Molecular weight formula_weight	12453.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M
Atom count atom_count	4188

MDILMTQTPLYLPVSLGDQASISCRSSQTIVHNNGNTYLEWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYYCFQGSHFPPTFGGGTKLEIA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	immunoglobulin heavy chain variable region
Molecular weight formula_weight	13552.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I

EVQLQQSGPELKKPGETVKISCKATNYAFTDYSMHWVKQAPGGDLKYVGWINTETDEPTFADDFKGRFAFSLDTSTSTAFLQINNLKNEDTATYFCVRDRHDYGEIFTYWGQGTTVTVSA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	530

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1n4xh1
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	d1n4xh2
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	d1n4xh3
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	d1n4xi1
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	d1n4xi2
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	d1n4xi3
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	d1n4xl1
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	d1n4xl2
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	d1n4xm1
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	d1n4xm2
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

CATH v4.4 (4 domains)

Domain ID domain_id	1n4xH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1n4xI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1n4xL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1n4xM00
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	126.930 Å
Unit-cell length b length_b	61.210 Å
Unit-cell length c length_c	57.300 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2560

fit	/app/data/saxs_computation/n4/1n4x/1n4x.fit
pddf	/app/data/pr_computation/n4/1n4x/1n4x.pr.out
profile	/app/data/saxs_computation/n4/1n4x/1n4x.dat

Structure of scFv 1696 at acidic pH

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

immunoglobulin kappa chain variable region

State in the Current Structure

Other States of the Same Protein in the Database

immunoglobulin heavy chain variable region

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)