3P6Z Hydrolase Hydrolase Inhibitor date Oct 11, 2010
title Structural Basis Of Thrombin Mediated Factor V Activation: E Role Of The Hirudin-Like Sequence Glu666-Glu672 For Process Heavy Chain-B Domain Junction
authors M.A.Corral-Rodriguez, P.E.Bock, E.Hernandez-Carvajal, R.Gutierr Gallego, P.Fuentes-Prior
compound source
Molecule: Thrombin Light Chain
Chain: A, G
Fragment: Thrombin Light Chain
Synonym: Coagulation Factor II, Thrombin Light Chain
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Purified From Blood Plasma

Molecule: Thrombin Heavy Chain
Chain: B, H
Fragment: Thrombin Heavy Chain
Synonym: Coagulation Factor II, Thrombin Heavy Chain

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Purified From Blood Plasma

Molecule: Coagulation Factor V
Chain: C, I
Fragment: Factor V, A2-B Domain Linker
Synonym: Activated Protein C Cofactor
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F5
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 1
R_factor 0.200 R_Free 0.239
length a length b length c angle alpha angle beta angle gamma
52.208 62.259 67.510 99.38 110.46 92.26
method X-Ray Diffractionresolution 1.70 Å
ligand 0G6, CL, MPD, NA, NAG enzyme Hydrolase E.C. BRENDA
A, G

H, B

Primary referenceStructural basis of thrombin-mediated factor V activation: the Glu666-Glu672 sequence is critical for processing at the heavy chain-B domain junction., Corral-Rodriguez MA, Bock PE, Hernandez-Carvajal E, Gutierrez-Gallego R, Fuentes-Prior P, Blood. 2011 May 9. PMID:21555742
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (3p6z.pdb1.gz) 114 Kb
  • Biological Unit Coordinates (3p6z.pdb2.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 3P6Z
  • CSU: Contacts of Structural Units for 3P6Z
  • Structure Factors (1204 Kb)
  • Retrieve 3P6Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3P6Z from S2C, [Save to disk]
  • Re-refined 3p6z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3P6Z 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 3P6Z
  • 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 3P6Z, from MSDmotif at EBI
  • Fold representative 3p6z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3p6z_B] [3p6z_H] [3p6z_C] [3p6z] [3p6z_G] [3p6z_I] [3p6z_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3P6Z: [Tryp_SPc ] by SMART
  • Other resources with information on 3P6Z
  • Community annotation for 3P6Z at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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