3kcg

Crystal structure of the antithrombin-factor IXa-pentasaccharide complex

Method: X-RAY DIFFRACTION

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

Coagulation factor IXa light chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 4	Antithrombin-III × 1 （P01008） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside ; × 1 CALCIUM ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 3	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, 2
Chains and sequence ranges	Author chain L； PDBConstruct 2–59； UniProt 131–188 Author chain H； PDBConstruct 1–235； UniProt 227–461

Antithrombin-III

Homo sapiens

UniProt P01008

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 4	Coagulation factor IXa light chain × 1 （P00740） Coagulation factor IXa heavy chain × 1 （P00740） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside ; × 1 CALCIUM ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ANT3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–432； UniProt 33–464

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	3kcg
Deposition date deposition_date	2009-10-21
Structure title title	Crystal structure of the antithrombin-factor IXa-pentasaccharide complex
Keywords keywords	;Michaelis complex, Blood coagulation, Calcium, Disulfide bond, EGF-like domain, Glycoprotein, Hemophilia, Hydrolase, Pharmaceutical, Protease, Secreted, Serine protease, Sulfation, Zymogen, Heparin-binding, Protease inhibitor, Serine protease inhibitor, Thrombophilia, HYDROLASE INHIBITOR ;; HYDROLASE, HYDROLASE INHIBITOR
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.

3kcg__assembly_1__model_1

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

Download this curve (.dat)

3kcg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kcg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.20 Å
Rg (electron density)	35.08 Å
Total Rg	35.46 Å
Atom count	5695
Residues	707
Excluded volume	101440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kcg__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 (9)

Entity 1 Entity 1 polymer

Description description	Coagulation factor IXa light chain
Molecular weight formula_weight	6470.4 kDa
EC 编号 ec_number	3.4.21.22
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	6669

MDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSK

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	Coagulation factor IXa heavy chain
Molecular weight formula_weight	26174.8 kDa
EC 编号 ec_number	3.4.21.22
Mutation mutation	S195A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDAGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT

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	Antithrombin-III
Molecular weight formula_weight	49085.0 kDa
Mutation mutation	S137A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKANKASKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMGRVANPCVK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 4 Entity 4 branched

Description description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	367.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 branched

Description description	;3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside ;
Molecular weight formula_weight	1661.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	667

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3kcgh_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d3kcgi_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

Domain ID domain_id	d3kcgl_
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

CATH v4.4 (5 domains)

Domain ID domain_id	3kcgH01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3kcgH02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3kcgI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

Domain ID domain_id	3kcgI02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

Domain ID domain_id	3kcgL00
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	78.780 Å
Unit-cell length b length_b	88.440 Å
Unit-cell length c length_c	147.230 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	1.700 Å
Low-resolution limit resolution_low	38.050 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2300

Crystal structure of the antithrombin-factor IXa-pentasaccharide complex

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

Coagulation factor IXa light chain

State in the Current Structure

Other States of the Same Protein in the Database

Antithrombin-III

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

3kcg__assembly_1__model_1

3kcg__assembly_1__model_1 | I(q)

3kcg__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 (9)

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

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of the antithrombin-factor IXa-pentasaccharide complex

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

Coagulation factor IXa light 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

Antithrombin-III

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

3kcg__assembly_1__model_1

3kcg__assembly_1__model_1 | I(q)

3kcg__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 (9)

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

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

CATH v4.4 (5 domains)

7. Citations (1)