SAXSdb — 3cxd

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

a peptide from osteopontin

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	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 40–51	Not recorded	Fab fragment of anti-osteopontin antibody 23C3, Light chain × 1 Fab fragment of anti-osteopontin antibody 23C3, Heavy chain × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；0.2M di-sodium tartrate, 20% PEG3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.292

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 3CXD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DSF Crystal structure of anti-osteopontin antibody 23C3 in complex with W43A mutated epitope peptide Deposited 2008-07-12	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 40–51（12 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；0.2M di-ammonium hydrogen phosphate, 20% PEG3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.297
9EOU Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide. Deposited 2024-03-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 153–168（16 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M sodium malonate pH 6.0, 9% w/v PEG 3350	Resolution 1.55 Å R-free 0.202

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

View Construct and Data Evidence

UniProt name	OSTP_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–12； UniProt 40–51

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	3cxd
Deposition date deposition_date	2008-04-24
Structure title title	Crystal structure of anti-osteopontin antibody 23C3 in complex with its epitope peptide
Keywords keywords	Fab, osteopontin, OPN, antibody-antigen complex, 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	26.17 Å
Radius of gyration Rg (electron density) rg_electron	25.30 Å
Forward intensity I(0) i0	39728600.00
Molecular weight molecular_weight	47941.0 kDa
Excluded volume excluded_volume	59529 Å³
Envelope volume envelope_volume	75364 Å³
Hydration-shell volume shell_volume	25282 Å³
Envelope diameter envelope_diameter	100.2 Å
Shell Rg shell_rg	31.88 Å
Envelope Rg envelope_rg	25.28 Å
Shape Rg shape_rg	25.28 Å
Total Rg total_rg	26.11 Å
Total atoms total_atoms	3373
Residues n_residues	438
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	95.5 Å
Rg (real space) rg_real	26.23 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	3.9730e+07
I(0) uncertainty (real space) i0_real_error	6.3030e+05
Rg (reciprocal space) rg_reciprocal	26.21 Å
I(0) (reciprocal space) i0_reciprocal	39730000.0000
Solution quality estimate total_estimate	0.8460
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.214
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8286000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.842; Smooth: 0.939

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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 fragment of anti-osteopontin antibody 23C3, Light chain
Molecular weight formula_weight	23070.4 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	3373

YIQMTQSPASLSVSVGETVTITCRASENIYSFLAWYQQKQGKSPQLLVYAATNLADGVPSRFSGSGSGTQFSLKINSLQSEDFGTYYCQHFWGTPFTFGSGTKLEIKRSDAAPTVSIFPPSAAQLSSGGGSVVCFLNNFYPKDINVKWKIDGAERGNGVLNSWTSQDSADSTYSMSSTLTSGGDEYERHNSYTCEATHKTSTSPIVKSFNRAA

Entity 2 Entity 2 polymer

Description description	Fab fragment of anti-osteopontin antibody 23C3, Heavy chain
Molecular weight formula_weight	23132.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVESGGGLVQPKGSLKISCAASGFTFNIYAMNWVRQAPGKGLEWVARIRSQSNNYTTYYADSVKDRFTISRDDSQSMLYLQMNNLKTEDTAMYYCVRQMGDYWGQGTTLTVSSAVKTPPSVYPLAPGGGAISNSMVTLGCLVNGYFPEPVTVTWNAGSLGSGVHTFPAVLQSDLYTLSSSVTVPVSTWPSEAVTCNVAHPASATSVDKAISPV

Entity 3 Entity 3 polymer

Description description	a peptide from osteopontin
Molecular weight formula_weight	1356.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

VATWLNPDPSQK

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3cxdH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3cxdH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3cxdL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3cxdL02
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	42.318 Å
Unit-cell length b length_b	92.020 Å
Unit-cell length c length_c	122.483 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	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2510
R_work r_work	0.2480
R_free r_free	0.2920

fit	/app/data/saxs_computation/cx/3cxd/3cxd.fit
pddf	/app/data/pr_computation/cx/3cxd/3cxd.pr.out
profile	/app/data/saxs_computation/cx/3cxd/3cxd.dat

Crystal structure of anti-osteopontin antibody 23C3 in complex with its epitope peptide

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

a peptide from osteopontin

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 polymer

Polymer Polymer

Entity 4 Entity 4 branched

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)