2GD4

Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex

PDB DOI: https://doi.org/10.2210/pdb2GD4/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-03-15 Released: 2006-05-09
Deposition Author(s): Johnson, D.J., Li, W., Adams, T.E., Huntington, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.298
R-Value Work: 0.247

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 173.13 kDa
Atom Count: 11,165
Modelled Residue Count: 1,414
Deposited Residue Count: 1,484
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain	A [auth L], D [auth A]	58	Homo sapiens	Mutation(s): 0 Gene Names: F10 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
PHAROS: P00742 GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain	B [auth H], E [auth B]	241	Homo sapiens	Mutation(s): 1 Gene Names: F10 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
PHAROS: P00742 GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	C [auth I], F [auth C]	443	Homo sapiens	Mutation(s): 4 Gene Names: SERPINC1, AT3
UniProt & NIH Common Fund Data Resources
Find proteins for P01008 (Homo sapiens) Explore P01008 Go to UniProtKB: P01008
PHAROS: P01008 GTEx: ENSG00000117601
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01008
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D]	6		N-Glycosylation	Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth E]	2		N-Glycosylation	Interactions Focus chain H [auth E] Interactions & Density Focus chain H [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside	I [auth F], J [auth G]	5		N/A	Interactions Focus chain I [auth F] Focus chain J [auth G] Interactions & Density Focus chain I [auth F] Focus chain J [auth G]
Glycosylation Resources
GlyTouCan: G25282IW GlyCosmos: G25282IW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth I] SDF format, chain M [auth I] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain L [auth I] MOL2 format, chain M [auth I] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C]	L [auth I], M [auth I], O [auth C], P [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth I] Focus chain M [auth I] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain L [auth I] Focus chain M [auth I] Focus chain O [auth C] Focus chain P [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain N [auth B] MOL2 format, chain K [auth H] MOL2 format, chain N [auth B]	K [auth H], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth H] Focus chain N [auth B] Interactions & Density Focus chain K [auth H] Focus chain N [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900028 Query on PRD_900028	I [auth F], J [auth G]	fondaparinux	Oligosaccharide / Anticoagulant		Interactions Focus chain I [auth F] Focus chain J [auth G] Interactions & Density Focus chain I [auth F] Focus chain J [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.298
R-Value Work: 0.247
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 220.263	α = 90
b = 60.588	β = 113.14
c = 156.174	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-05-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-05-09
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-07-12
Changes: Advisory, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
Version 2.1: 2021-10-20
Changes: Advisory, Database references, Structure summary
Version 2.2: 2023-08-30
Changes: Data collection, Refinement description
Version 2.3: 2024-03-13
Changes: Source and taxonomy, Structure summary