3BEF Hydrolase date Nov 17, 2007
title Crystal Structure Of Thrombin Bound To The Extracellular Fra Par1
authors P.S.Gandhi, A.Bah, Z.Chen, F.S.Mathews, E.Di Cera
compound source
Molecule: Prothrombin
Chain: A, D
Fragment: Thrombin Light Chain
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F2
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029

Molecule: Prothrombin
Chain: B, E
Fragment: Thrombin Heavy Chain
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F2
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029

Molecule: Proteinase-Activated Receptor 1
Chain: C, F
Fragment: Unp Residues 49-57
Synonym: Par-1, Thrombin Receptor, Coagulation Factor II Re
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F2r, Cf2r, Par1, Tr
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
symmetry Space Group: P 1
R_factor 0.207 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.060 50.342 85.078 76.89 84.30 73.69
method X-Ray Diffractionresolution 2.20 Å
ligand NAG enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


Primary referenceStructural identification of the pathway of long-range communication in an allosteric enzyme., Gandhi PS, Chen Z, Mathews FS, Di Cera E, Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1832-7. Epub 2008 Feb 4. PMID:18250335
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (3bef.pdb1.gz) 54 Kb
  • Biological Unit Coordinates (3bef.pdb2.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 3BEF
  • CSU: Contacts of Structural Units for 3BEF
  • Likely Quarternary Molecular Structure file(s) for 3BEF
  • Structure Factors (490 Kb)
  • Retrieve 3BEF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BEF from S2C, [Save to disk]
  • Re-refined 3bef structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BEF 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 3BEF
  • 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
  • 3D motif for 3BEF, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bef_D] [3bef_B] [3bef_C] [3bef_E] [3bef_F] [3bef_A] [3bef]
  • SWISS-PROT database: [P25116] [P00734]
  • Domain organization of [PAR1_HUMAN] [THRB_HUMAN] by SWISSPFAM
  • Domain found in 3BEF: [Tryp_SPc ] by SMART
  • Other resources with information on 3BEF
  • Community annotation for 3BEF 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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