3JTC Blood Clotting date Sep 11, 2009
title Importance Of Mg2+ In The Ca2+-Dependent Folding Of The Gamm Carboxyglutamic Acid Domains Of Vitamin K-Dependent Clottin Anticlotting Proteins
authors S.P.Bajaj, K.Vadivel, S.Agah, D.Cascio, S.Krishnaswamy, C.Esmon, K.Padmanabhan
compound source
Molecule: Endothelial Protein C Receptor
Chain: A, B
Fragment: Extracellular Domain (Unp Residues 18-210)
Synonym: Endothelial Cell Protein C Receptor, Activated Pro Receptor, Apc Receptor;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Vitamin K-Dependent Protein C
Chain: C, D
Fragment: Gla Domain (Unp Residues 43-75)
Synonym: Autoprothrombin Iia, Anticoagulant Protein C, Bloo Coagulation Factor Xiv, Vitamin K-Dependent Protein C Light Vitamin K-Dependent Protein C Heavy Chain, Activation Pepti
Ec: 3.4.21.69

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Cleavage Happened During Crystallization And Crystal Contains Only The N-Terminal Domain (Gla Domain) Of C.
symmetry Space Group: P 1 21 1
R_factor 0.191 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.220 62.360 71.030 90.00 101.81 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand CA, CGU, MG, NAG, NDG, PTY enzyme Hydrolase E.C.3.4.21.69 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceStructural and Functional Studies of gamma-Carboxyglutamic Acid Domains of Factor VIIa and Activated Protein C: Role of Magnesium at Physiological Calcium., Vadivel K, Agah S, Messer AS, Cascio D, Bajaj MS, Krishnaswamy S, Esmon CT, Padmanabhan K, Bajaj SP, J Mol Biol. 2013 Feb 20. pii: S0022-2836(13)00104-6. doi:, 10.1016/j.jmb.2013.02.017. PMID:23454357
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (3jtc.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (3jtc.pdb2.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 3JTC
  • CSU: Contacts of Structural Units for 3JTC
  • Structure Factors (878 Kb)
  • Retrieve 3JTC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JTC from S2C, [Save to disk]
  • Re-refined 3jtc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3JTC in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3JTC
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3JTC, from MSDmotif at EBI
  • Fold representative 3jtc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jtc_C] [3jtc_D] [3jtc] [3jtc_B] [3jtc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3JTC
  • Community annotation for 3JTC at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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