SAXSdb — 1iod

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

COAGULATION FACTOR X GLA DOMAIN

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 41–84	Fragment：GLA DOMAIN(RESIDUES 41-84) Non-standard monomer：Yes (specific site not provided by mmCIF)	COAGULATION FACTOR X BINDING PROTEIN × 1 COAGULATION FACTOR X BINDING PROTEIN × 1 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
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain G； UniProt 41–84	Fragment：GLA DOMAIN(RESIDUES 41-84) Non-standard monomer：Yes (specific site not provided by mmCIF)	COAGULATION FACTOR X BINDING PROTEIN × 2 COAGULATION FACTOR X BINDING PROTEIN × 2 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
3	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain G； UniProt 41–84	Fragment：GLA DOMAIN(RESIDUES 41-84) Non-standard monomer：Yes (specific site not provided by mmCIF)	COAGULATION FACTOR X BINDING PROTEIN × 2 COAGULATION FACTOR X BINDING PROTEIN × 2 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

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 1IOD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1APO 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 Deposited 1992-04-21	Different construct Different mutation/modification 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 85–126（42 aa）	Not recorded	OH HYDROXIDE ION × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
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 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 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
1KIG BOVINE FACTOR XA Deposited 1997-04-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions 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 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 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 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 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FA10_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–44； UniProt 41–84

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	1iod
Deposition date deposition_date	2001-02-27
Structure title title	CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X
Keywords keywords	calcium bridging, domain swapping, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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	21.82 Å
Radius of gyration Rg (electron density) rg_electron	21.02 Å
Forward intensity I(0) i0	23199500.00
Molecular weight molecular_weight	35447.0 kDa
Excluded volume excluded_volume	43492 Å³
Envelope volume envelope_volume	49409 Å³
Hydration-shell volume shell_volume	20389 Å³
Envelope diameter envelope_diameter	81.4 Å
Shell Rg shell_rg	26.92 Å
Envelope Rg envelope_rg	21.31 Å
Shape Rg shape_rg	21.00 Å
Total Rg total_rg	21.80 Å
Total atoms total_atoms	2472
Residues n_residues	284
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	77.9 Å
Rg (real space) rg_real	21.91 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	2.3200e+07
I(0) uncertainty (real space) i0_real_error	3.7880e+05
Rg (reciprocal space) rg_reciprocal	21.89 Å
I(0) (reciprocal space) i0_reciprocal	23200000.0000
Solution quality estimate total_estimate	0.7597
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.497
Kurtosis Kurtosis kurtosis	-0.059
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5871000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.682; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	COAGULATION FACTOR X BINDING PROTEIN
Molecular weight formula_weight	14682.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2653

DCSSGWSSYEGHCYKVFKQSKTWADAESFCTKQVNGGHLVSIESSGEADFVGQLIAQKIKSAKIHVWIGLRAQNKEKQCSIEWSDGSSISYENWIEEESKKCLGVHIETGFHKWENFYCEQQDPFVCEA

Entity 2 Entity 2 polymer

Description description	COAGULATION FACTOR X BINDING PROTEIN
Molecular weight formula_weight	14580.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DCPSDWSSYEGHCYKPFNEPKNWADAENFCTQQHTGSHLVSFQSTEEADFVVKLAFQTFDYGIFWMGLSKIWNQCNWQWSNAAMLKYTDWAEESYCVYFKSTNNKWRSITCRMIANFVCEFQA

Entity 3 Entity 3 polymer

Description description	COAGULATION FACTOR X GLA DOMAIN
Molecular weight formula_weight	5734.7 kDa
EC 编号 ec_number	3.4.21.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

ANSFLEEVKQGNLERECLEEACSLEEAREVFEDAEQTDEFWSKY

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1ioda_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1iodb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1iodg_
Class class	g — Small proteins
Fold Fold fold	g.32 — GLA-domain
Superfamily Superfamily superfamily	g.32.1 — GLA-domain
Family Family family	g.32.1.1 — GLA-domain

CATH v4.4 (2 domains)

Domain ID domain_id	1iodA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1iodB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (1)

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Unit-cell length a length_a	99.760 Å
Unit-cell length b length_b	99.760 Å
Unit-cell length c length_c	90.420 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2670

fit	/app/data/saxs_computation/io/1iod/1iod.fit
pddf	/app/data/pr_computation/io/1iod/1iod.pr.out
profile	/app/data/saxs_computation/io/1iod/1iod.dat

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X

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

COAGULATION FACTOR X GLA DOMAIN

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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)