SAXSdb — 1sdd

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

Coagulation factor V

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CALCIUM ION × 1 COPPER (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA5_BOVIN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 29–334 Author chain B； PDBConstruct 1–647； UniProt 1565–2211

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	1sdd
Deposition date deposition_date	2004-02-13
Structure title title	Crystal Structure of Bovine Factor Vai
Keywords keywords	COAGULATION, COPPER-BINDING PROTEIN, COFACTOR, BLOOD CLOTTING; BLOOD CLOTTING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1sdd__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1sdd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1sdd__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.87 Å
Rg (electron density)	31.12 Å
Total Rg	31.63 Å
Atom count	7082
Residues	869
Excluded volume	126040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1sdd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Coagulation factor V
Molecular weight formula_weight	34730.4 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	7271

AKLRQFYVAAQSIRWNYRPESTHLSSKPFETSFKKIVYREYEAYFQKEKPQSRTSGLLGPTLYAEVGDIMKVHFKNKAHKPLSIHAQGIKYSKFSEGASYSDHTLPMEKMDDAVAPGQEYTYEWIISEHSGPTHDDPPCLTHIYYSYVNLVEDFNSGLIGPLLICKKGTLTEDGTQKMFEKQHVLMFAVFDESKSWNQTSSLMYTVNGYVNGTMPDITVCAHDHISWHLIGMSSGPELFSIHFNGQVLEQNHHKISAITLVSATSTTANMTVSPEGRWTIASLIPRHFQAGMQAYIDIKNCAKKTR

Entity 2 Entity 2 polymer

Description description	Coagulation factor V
Molecular weight formula_weight	74711.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNTGNRKYYYIAAEEISWDYSKFVQSDDVDYVPEDTVYKKVVFRKYLDSTFTKLDPQGEYEEHLGILGPVIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEWFKEDNAIQPNKTYTYVWHATTRSGPENPGSACRAWAYYSAVNPEKDIHSGLIGPLLICRKGTLDKETNMPVDMREFVLLFMVFDEKKSWYYDKKPTRSWRRASSEVKNSHEFHAINGMIYNLPGLRMYEQEWVRLHLLNLGGSRDIHVVHFHGQTLLENGTQQHQLGVWPLLPGSFKTLEMKASKPGWWLLDTEVGEIQRAGMQTPFLIVDRECKMPMGLSTGLIADSQIQASEFWGYWEPKLARLNNGGSYNAWIAEKLSTEFNPEPWIQVDMQKEVLLTGIQTQGAKHYLKPYYTTEFCVAYSLDRKNWRIFKGNSTRNVMYFGGNSDASTIKENQIDPPVVARYIRISPTGSYNKPALRLELQGCEVNGCSTPLGMESGKIENKQITASSFKKSWWGNYWEPFLARLNAQGRVNAWQAKANNNNQWLQIDLLKIKKITAIVTQGCKSLSSEMYVKSYTIHYSDQGTDWKPYREKSSMVDKIFEGNNNVRGHVKNFFNPPIISRFIRIIPKTWNQSIALRLELFGCDMY

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

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	1

Entity 5 Entity 5 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	189

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1sdda1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d1sdda2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d1sddb1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d1sddb2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d1sddb3
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.2 — Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)

Domain ID domain_id	d1sddb4
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.2 — Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain)

CATH v4.4 (6 domains)

Domain ID domain_id	1sddA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1sddA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1sddB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1sddB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1sddB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	1sddB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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Unit-cell length a length_a	63.370 Å
Unit-cell length b length_b	86.560 Å
Unit-cell length c length_c	229.200 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	30.000 Å
R factor r_factor	0.2620
R_work r_work	0.2520
R_free r_free	0.2960

Crystal Structure of Bovine Factor Vai

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

Coagulation factor V

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1sdd__assembly_1__model_1

1sdd__assembly_1__model_1 | I(q)

1sdd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Bovine Factor Vai

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

Coagulation factor V

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1sdd__assembly_1__model_1

1sdd__assembly_1__model_1 | I(q)

1sdd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)