SAXSdb — 1apo

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

EGF-LIKE MODULE OF BLOOD COAGULATION FACTOR X

Bos taurus

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 85–126	Not recorded	OH HYDROXIDE ION × 1	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	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 1APO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CCF How an Epidermal Growth Factor (EGF)-Like Domain Binds Calcium-High Resolution NMR Structure of the Calcium Form of the NH2-Terminal EGF-Like Domain in Coagulation Factor X Deposited 1993-05-19	Different mutation/modification Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 85–126（42 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1IOD CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X Deposited 2001-02-27	Different construct Different mutation/modification 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 G 41–84（44 aa） Fragment：GLA DOMAIN(RESIDUES 41-84)	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；PEG8000, calcium chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.267
1IOD CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X Deposited 2001-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 41–84（44 aa） Fragment：GLA DOMAIN(RESIDUES 41-84)	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；PEG8000, calcium chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.267
1IOD CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X Deposited 2001-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 41–84（44 aa） Fragment：GLA DOMAIN(RESIDUES 41-84)	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；PEG8000, calcium chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.267
1KIG BOVINE FACTOR XA Deposited 1997-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 234–474（241 aa） Chain L 129–179（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1WHE COAGULATION FACTOR, NMR, 20 STRUCTURES Deposited 1996-06-18	Different construct Different mutation/modification Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–126（86 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1WHF COAGULATION FACTOR, NMR, 15 STRUCTURES Deposited 1996-06-18	Different construct Different mutation/modification Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–126（86 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

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

View Construct and Data Evidence

UniProt name	FA10_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–42； UniProt 85–126

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	1apo
Deposition date deposition_date	1992-04-21
Structure title title	THREE-DIMENSIONAL STRUCTURE OF THE APO FORM OF THE N-TERMINAL EGF-LIKE MODULE OF BLOOD COAGULATION FACTOR X AS DETERMINED BY NMR SPECTROSCOPY AND SIMULATED FOLDING
Keywords keywords	COAGULATION FACTOR; COAGULATION FACTOR
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	10.85 Å
Radius of gyration Rg (electron density) rg_electron	11.27 Å
Forward intensity I(0) i0	73226000.00
Molecular weight molecular_weight	59383.0 kDa
Excluded volume excluded_volume	69285 Å³
Envelope volume envelope_volume	12676 Å³
Hydration-shell volume shell_volume	8485 Å³
Envelope diameter envelope_diameter	51.8 Å
Shell Rg shell_rg	18.42 Å
Envelope Rg envelope_rg	14.90 Å
Shape Rg shape_rg	11.30 Å
Total Rg total_rg	11.48 Å
Total atoms total_atoms	7592
Residues n_residues	546
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	29.6 Å
Rg (real space) rg_real	10.21 Å
Rg uncertainty (real space) rg_real_error	0.05 Å
I(0) (real space) i0_real	7.0280e+07
I(0) uncertainty (real space) i0_real_error	5.7630e+05
Rg (reciprocal space) rg_reciprocal	11.07 Å
I(0) (reciprocal space) i0_reciprocal	73230000.0000
Solution quality estimate total_estimate	0.6775
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	10.1 Å
Skewness Skewness skewness	0.412
Kurtosis Kurtosis kurtosis	-0.502
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.2720
Highest regularization parameter α highest_alpha	28300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.986; Stabil: 0.978; Sysdev: 0.000; Positv: 1.000; Valcen: 0.919; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1apoa_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

CATH v4.4 (1 domains)

Domain ID domain_id	1apoA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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8. Citations (3)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	EGF-LIKE MODULE OF BLOOD COAGULATION FACTOR X
Molecular weight formula_weight	4560.9 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	7592

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913

THREE-DIMENSIONAL STRUCTURE OF THE APO FORM OF THE N-TERMINAL EGF-LIKE MODULE OF BLOOD COAGULATION FACTOR X AS DETERMINED BY NMR SPECTROSCOPY AND SIMULATED FOLDING

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

EGF-LIKE MODULE OF BLOOD COAGULATION FACTOR X

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	HYDROXIDE ION
Molecular weight formula_weight	17.0 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/ap/1apo/1apo.fit
pddf	/app/data/pr_computation/ap/1apo/1apo.pr.out
profile	/app/data/saxs_computation/ap/1apo/1apo.dat