1IXX | pdb_00001ixx

CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS

• PDB DOI: https://doi.org/10.2210/pdb1IXX/pdb

• Classification: COAGULATION FACTOR BINDING
• Organism(s): Protobothrops flavoviridis
• Mutation(s): No 


• Deposited: 1997-05-01 Released: 1998-05-06 
• Deposition Author(s): Mizuno, H., Fujimoto, Z., Koizumi, M., Kano, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.221 (Depositor) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains.

Mizuno, H., Fujimoto, Z., Koizumi, M., Kano, H., Atoda, H., Morita, T.

(1997) Nat Struct Biol 4: 438-441

• PubMed: 9187649 
• DOI: https://doi.org/10.1038/nsb0697-438
• Primary Citation Related Structures: 
  1IXX


• PubMed Abstract: 
  

  Coagulation factors IX/X-binding protein is an intertwined dimer with a central loop projecting into the adjoining subunit. Excluding this loop, each subunit has a fold similar to rat mannose-binding protein.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.14 kDa 
• Atom Count: 6,329 
• Modeled Residue Count: 756 
• Deposited Residue Count: 756 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTORS IX/X-BINDING PROTEIN	A, C, E	129	Protobothrops flavoviridis	Mutation(s): 0
UniProt
Find proteins for P23806 (Protobothrops flavoviridis) Explore P23806  Go to UniProtKB:  P23806

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTORS IX/X-BINDING PROTEIN	B, D, F	123	Protobothrops flavoviridis	Mutation(s): 0
UniProt
Find proteins for P23807 (Protobothrops flavoviridis) Explore P23807  Go to UniProtKB:  P23807

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.221 (Depositor) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.2	α = 90
b = 85.7	β = 90
c = 65.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-06 
Deposition Author(s): Mizuno, H., Fujimoto, Z., Koizumi, M., Kano, H.

Revision History  

• Version 1.0: 1998-05-06
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary