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
  • Alignments of the sequence of 3JTC with the sequences similar proteins can be viewed for 3JTC's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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