1J34

Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

Structural Biology Knowledgebase: 1J34 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 1J34

Classification: Protein binding / Blood clotting

Total Structure Weight: 35641.30

Macromolecule Entities
Molecule Chains Length Organism Details
coagulation factor IX-binding protein A chain A 129 Protobothrops flavoviridis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
coagulation factor IX-binding protein B chain B 123 Protobothrops flavoviridis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Coagulation factor IX C 46 Bos taurus EC#: 3.4.21.22 IUBMB
Fragment: GLA DOMAIN
Mutation: E407X, E408X, E415X, E417X, E420X, E421X, E426X, E427X, E430X, E433X, E436X, E440X
Gene Name(s): F9 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CA
Query on CA

A, B, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CGU
Query on CGU
C L-PEPTIDE LINKING C6 H9 N O6 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.183
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.55 α = 90.00
b = 37.20 β = 103.56
c = 62.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-20
  • Released Date: 2003-07-08
  • Deposition author(s): Shikamoto, Y., Morita, T., Fujimoto, Z., Mizuno, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4