SAXSdb — 1nl0

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

factor IX

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	anti-factor IX antibody, 10C12, chain L × 1 anti-factor IX antibody, 10C12, chain H × 1 SULFATE ION × 1 CALCIUM ION × 6 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	anti-factor IX antibody, 10C12, chain L × 2 anti-factor IX antibody, 10C12, chain H × 2 SULFATE ION × 2 CALCIUM ION × 12 water × 6	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	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–45； UniProt 47–91

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	1nl0
Deposition date deposition_date	2003-01-06
Structure title title	Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12
Keywords keywords	IMMUNE SYSTEM, ANTIBODY, GLA DOMAIN; IMMUNE SYSTEM
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.

1nl0__assembly_1__model_1

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

Download this curve (.dat)

1nl0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nl0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.98 Å
Rg (electron density)	26.36 Å
Total Rg	27.11 Å
Atom count	3651
Residues	462
Excluded volume	64640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nl0__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nl0__assembly_2__model_1`	hexameric （6）	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	anti-factor IX antibody, 10C12, chain L
Molecular weight formula_weight	22631.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3799

QSVLTQPPSVSAAPGQKVTISCSGSTSNIGNNYVSWYQQHPGKAPKLMIYDVSKRPSGVPDRFSGSKSGNSASLDISGLQSEDEADYYCAAWDDSLSEFLFGTGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT

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 polymer

Description description	anti-factor IX antibody, 10C12, chain H
Molecular weight formula_weight	23800.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GVQLVESGGGVVQPGRSLRLSCAASGFTFSTYAMHWVRQAPGKGLEWVAIISYDGSKKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARASIAAARVLDYWGRGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

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 3 Entity 3 polymer

Description description	factor IX
Molecular weight formula_weight	7117.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

YNSGKLEEFVQGNLERECMEEKCSFEEAREVFENTERTTEFWKQYEEEEEE

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1nl0g_
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

Domain ID domain_id	d1nl0h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1nl0h2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1nl0l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1nl0l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	1nl0H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1nl0H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1nl0L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1nl0L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	105.089 Å
Unit-cell length b length_b	71.614 Å
Unit-cell length c length_c	90.867 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.14 °
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	2.200 Å
Low-resolution limit resolution_low	24.660 Å
R factor r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2700

Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12

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

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

1nl0__assembly_1__model_1

1nl0__assembly_1__model_1 | I(q)

1nl0__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12

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

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

1nl0__assembly_1__model_1

1nl0__assembly_1__model_1 | I(q)

1nl0__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)