3D67 Hydrolase date May 19, 2008
title Crystal Structure Of Thrombin-Activatable Fibrinolysis Inhib (Tafi) In Complex With 2-Guanidino-Ethyl-Mercaptosuccinic A (Gemsa)
authors T.H.C.Brondijk, E.G.Huizinga
compound source
Molecule: Carboxypeptidase B2
Chain: A, B, C
Fragment: Unp Residues 24-423
Synonym: Carboxypeptidase U, Cpu, Thrombin-Activable Fibrin Inhibitor, Tafi, Plasma Carboxypeptidase B, Pcpb;
Ec: 3.4.17.20
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cpb2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293es
Expression_system_cell: Embryonic Kidney Cell
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pabc345
symmetry Space Group: P 31 2 1
R_factor 0.198 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
161.050 161.050 138.990 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.40 Å
ligand GEM, NAG, ZN enzyme Hydrolase E.C.3.4.17.20 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceCrystal structures of TAFI elucidate the inactivation mechanism of activated TAFI; A novel mechanism for enzyme auto-regulation., Marx PF, Brondijk TH, Plug T, Romijn RA, Hemrika W, Meijers JC, Huizinga EG, Blood. 2008 Jun 17;. PMID:18559974
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (204 Kb) [Save to disk]
  • Biological Unit Coordinates (3d67.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (3d67.pdb2.gz) 67 Kb
  • Biological Unit Coordinates (3d67.pdb3.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 3D67
  • CSU: Contacts of Structural Units for 3D67
  • Likely Quarternary Molecular Structure file(s) for 3D67
  • Structure Factors (631 Kb)
  • Retrieve 3D67 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D67 from S2C, [Save to disk]
  • Re-refined 3d67 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D67 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 3D67
  • 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 3D67, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d67_C] [3d67] [3d67_B] [3d67_A]
  • SWISS-PROT database: [Q96IY4]
  • Domain organization of [CBPB2_HUMAN] by SWISSPFAM
  • Domain found in 3D67: [Zn_pept ] by SMART
  • Other resources with information on 3D67
  • Community annotation for 3D67 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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