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
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] (183 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
  • Alignments of the sequence of 3P6Z with the sequences similar proteins can be viewed for 3P6Z'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 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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