SAXSdb — 5vyg

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

Coagulation factor IX

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose × 1 CALCIUM ION × 2 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–42； UniProt 92–130 Author chain B； PDBConstruct 4–42； UniProt 92–130 Author chain C； PDBConstruct 4–42； UniProt 92–130

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	5vyg
Deposition date deposition_date	2017-05-25
Structure title title	Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide
Keywords keywords	Notch regulation, EGF repeat, glycosylation, Transferase-Hydrolase complex, transferase, hydrolase; transferase, hydrolase
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.

5vyg__assembly_1__model_1

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

Download this curve (.dat)

5vyg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vyg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	12.05 Å
Rg (electron density)	12.00 Å
Total Rg	13.03 Å
Atom count	354
Residues	43
Excluded volume	6188 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vyg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vyg__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5vyg__assembly_3__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Coagulation factor IX
Molecular weight formula_weight	5710.2 kDa
EC 编号 ec_number	3.4.21.22
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C
Atom count atom_count	1085

MDIVDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCELLEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose
Molecular weight formula_weight	444.4 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d5vyga1
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

Domain ID domain_id	d5vyga2
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	d5vyga3
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	d5vygb1
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

Domain ID domain_id	d5vygb2
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	d5vygb3
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	d5vygc1
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

Domain ID domain_id	d5vygc2
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	d5vygc3
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 (3 domains)

Domain ID domain_id	5vygA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	5vygB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	5vygC00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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Unit-cell length a length_a	92.417 Å
Unit-cell length b length_b	46.840 Å
Unit-cell length c length_c	37.259 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	46.160 Å
R factor r_factor	0.2145
R_work r_work	0.2123
R_free r_free	0.2590

Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide

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

Coagulation factor IX

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

5vyg__assembly_1__model_1

5vyg__assembly_1__model_1 | I(q)

5vyg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (9 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide

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

Coagulation factor IX

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

5vyg__assembly_1__model_1

5vyg__assembly_1__model_1 | I(q)

5vyg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (9 domains)

CATH v4.4 (3 domains)

7. Citations (1)