2CF9 Hydrolase Hydrolase Inhibitor date Feb 17, 2006
title Complex Of Recombinant Human Thrombin With An Inhibitor
authors E.Schweizer, A.Hoffmann-Roeder, J.A.Olsen, U.Obst-Sander, B.Wagn M.Kansy, D.W.Banner, F.Diederich
compound source
Molecule: Thrombin Heavy Chain
Chain: H
Fragment: Catalytic, Residues 364-620
Ec: 3.4.21.5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_cell_line: Ovary

Molecule: Hirudin Iiia
Chain: I
Fragment: C-Terminus, Residues 55-65
Engineered: Yes

Synthetic: Yes
Organism_scientific: Hirudo Medicinalis
Organism_common: Medicinal Leech
Organism_taxid: 6421

Molecule: Thrombin Light Chain
Chain: L
Fragment: Light Chain, Residues 334-361
Ec: 3.4.21.5
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_cell_line: Ovary
symmetry Space Group: C 1 2 1
R_factor 0.160 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.290 71.840 73.060 90.00 100.56 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand 348, CA, NA, SIN enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
H


L


Primary referenceMultipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors., Schweizer E, Hoffmann-Roder A, Olsen JA, Seiler P, Obst-Sander U, Wagner B, Kansy M, Banner DW, Diederich F, Org Biomol Chem. 2006 Jun 21;4(12):2364-75. Epub 2006 May 10. PMID:16763681
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (63 Kb) [Save to disk]
  • Biological Unit Coordinates (2cf9.pdb1.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 2CF9
  • CSU: Contacts of Structural Units for 2CF9
  • Likely Quarternary Molecular Structure file(s) for 2CF9
  • Structure Factors (240 Kb)
  • Retrieve 2CF9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2CF9 from S2C, [Save to disk]
  • Re-refined 2cf9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2CF9 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 2CF9
  • 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 2CF9, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2cf9_I] [2cf9_L] [2cf9_H] [2cf9]
  • SWISS-PROT database: [P00734]
  • Domain organization of [THRB_HUMAN] by SWISSPFAM
  • Domain found in 2CF9: [Tryp_SPc ] by SMART
  • Other resources with information on 2CF9
  • Community annotation for 2CF9 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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