1IOD | pdb_00001iod

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X

PDB DOI: https://doi.org/10.2210/pdb1IOD/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Deinagkistrodon acutus, Bos taurus
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2001-02-27 Released: 2001-06-27
Deposition Author(s): Mizuno, H., Fujimoto, Z., Atoda, H., Morita, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.267 (Depositor), 0.255 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X.

Mizuno, H., Fujimoto, Z., Atoda, H., Morita, T.

(2001) Proc Natl Acad Sci U S A 98: 7230-7234

PubMed: 11404471 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.131179698
Primary Citation Related Structures:
1IOD

PubMed Abstract:
The gamma-carboxyglutamic acid (Gla) domain of blood coagulation factors is responsible for Ca2+-dependent phospholipid membrane binding. Factor X-binding protein (X-bp), an anticoagulant protein from snake venom, specifically binds to the Gla domain of factor X. The crystal structure of X-bp in complex with the Gla domain peptide of factor X at 2.3-A resolution showed that the anticoagulation is based on the fact that two patches of the Gla domain essential for membrane binding are buried in the complex formation. The Gla domain thus is expected to be a new target of anticoagulant drugs, and X-bp provides a basis for designing them. This structure also provides a membrane-bound model of factor X.

Organizational Affiliation

Department of Biotechnology, National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602, Japan. mizuno@nias.affrc.go.jp

Macromolecule Content

Total Structure Weight: 35.48 kDa
Atom Count: 2,653
Modeled Residue Count: 296
Deposited Residue Count: 296
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X BINDING PROTEIN	A	129	Deinagkistrodon acutus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9IAM1 (Deinagkistrodon acutus) Explore Q9IAM1 Go to UniProtKB: Q9IAM1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9IAM1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X BINDING PROTEIN	B	123	Deinagkistrodon acutus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9DEF8 (Deinagkistrodon acutus) Explore Q9DEF8 Go to UniProtKB: Q9DEF8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9DEF8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X GLA DOMAIN	C [auth G]	44	Bos taurus	Mutation(s): 0 EC: 3.4.21.6 Membrane Entity: Yes
UniProt
Find proteins for P00743 (Bos taurus) Explore P00743 Go to UniProtKB: P00743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00743
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain O [auth G] SDF format, chain N [auth G] SDF format, chain M [auth G] SDF format, chain L [auth G] SDF format, chain K [auth G] SDF format, chain J [auth G] SDF format, chain I [auth G] SDF format, chain H [auth G] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain O [auth G] MOL2 format, chain N [auth G] MOL2 format, chain M [auth G] MOL2 format, chain L [auth G] MOL2 format, chain K [auth G] MOL2 format, chain J [auth G] MOL2 format, chain I [auth G] MOL2 format, chain H [auth G] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain O [auth G] mmCIF format, chain N [auth G] mmCIF format, chain M [auth G] mmCIF format, chain L [auth G] mmCIF format, chain K [auth G] mmCIF format, chain J [auth G] mmCIF format, chain I [auth G] mmCIF format, chain H [auth G] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth B] H [auth G] D [auth A], E [auth A], F [auth A], G [auth B], H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G], O [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU Query on CGU	C [auth G]	L-PEPTIDE LINKING	C₆ H₉ N O₆		GLU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.267 (Depositor), 0.255 (DCC)
R-Value Work: 0.201 (Depositor), 0.201 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.76	α = 90
b = 99.76	β = 90
c = 90.42	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2001-06-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-06-27
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description