SAXSdb — 1j34

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

coagulation factor IX-binding protein A chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	coagulation factor IX-binding protein B chain × 1 （P23807） Coagulation factor IX × 1 （P00741） CALCIUM ION × 7 MAGNESIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IXA_TRIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–129； UniProt 1–129

coagulation factor IX-binding protein B chain

OrganismNot specified

UniProt P23807

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	coagulation factor IX-binding protein A chain × 1 （P23806） Coagulation factor IX × 1 （P00741） CALCIUM ION × 7 MAGNESIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IXB_TRIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–123； UniProt 24–146

Coagulation factor IX

OrganismNot specified

UniProt P00741

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	coagulation factor IX-binding protein A chain × 1 （P23806） coagulation factor IX-binding protein B chain × 1 （P23807） CALCIUM ION × 7 MAGNESIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA9_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–46； UniProt 1–46

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	1j34
Deposition date deposition_date	2003-01-20
Structure title title	Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein
Keywords keywords	MAGNESIUM ION, CALCIUM ION, GLA DOMAIN, Protein binding-Blood clotting COMPLEX; Protein binding/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.

1j34__assembly_1__model_1

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

Download this curve (.dat)

1j34__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1j34__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.55 Å
Rg (electron density)	20.78 Å
Total Rg	21.51 Å
Atom count	2490
Residues	286
Excluded volume	43637 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1j34__assembly_1__model_1`	trimeric （3）	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 IX-binding protein A chain
Molecular weight formula_weight	14655.2 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	2934

DCPSGWSSYEGHCYKPFKLYKTWDDAERFCTEQAKGGHLVSIESAGEADFVAQLVTENIQNTKSYVWIGLRVQGKEKQCSSEWSDGSSVSYENWIEAESKTCLGLEKETGFRKWVNIYCGQQNPFVCEA

Entity 2 Entity 2 polymer

Description description	coagulation factor IX-binding protein B chain
Molecular weight formula_weight	14455.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DCPSDWSSYEGHCYKPFSEPKNWADAENFCTQQHAGGHLVSFQSSEEADFVVKLAFQTFGHSIFWMGLSNVWNQCNWQWSNAAMLRYKAWAEESYCVYFKSTNNKWRSRACRMMAQFVCEFQA

Entity 3 Entity 3 polymer

Description description	Coagulation factor IX
Molecular weight formula_weight	6177.3 kDa
EC 编号 ec_number	3.4.21.22
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

YNSGKLEEFVRGNLERECKEEKCSFEEAREVFENTEKTTEFWKQYV

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	7

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	444

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1j34a_
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	d1j34b_
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	d1j34c_
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	1j34A00
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	1j34B00
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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Unit-cell length a length_a	128.552 Å
Unit-cell length b length_b	37.204 Å
Unit-cell length c length_c	62.626 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	19.630 Å
R factor r_factor	0.1850
R_work r_work	0.1830
R_free r_free	0.2120

Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

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

coagulation factor IX-binding protein A chain

State in the Current Structure

Other States of the Same Protein in the Database

coagulation factor IX-binding protein B chain

State in the Current Structure

Other States of the Same Protein in the Database

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

1j34__assembly_1__model_1

1j34__assembly_1__model_1 | I(q)

1j34__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (3)

Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

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

coagulation factor IX-binding protein A chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

coagulation factor IX-binding protein B chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

1j34__assembly_1__model_1

1j34__assembly_1__model_1 | I(q)

1j34__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (3)