2C4F Hydrolase date Oct 18, 2005
title Crystal Structure Of Factor Vii.Stf Complexed With Pd0297121
authors J.T.Kohrt, E.Zhang
compound source
Molecule: Coagulation Factor Vii Precursor
Chain: H
Fragment: Factor Vii Heavy Chain, Residues 213-466
Synonym: Factor Vii, Serum Prothrombin Conversion Accelerator, Spca, Proconvertin, Eptacog Alfa;
Ec: 3.4.21.21
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Coagulation Factor Vii Precursor
Chain: L
Fragment: Factor Vii Light Chain, Residues 61-202
Synonym: Factor Vii, Serum Prothrombin Conversion Accelerator, Spca, Proconvertin, Eptacog Alfa;
Ec: 3.4.21.21

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Tissue Factor Precursor
Chain: T
Fragment: Factor III, Residues 38-112
Synonym: Tissue Factor, Tf, Coagulation Factor III Thromboplastin, Cd142 Antigen;

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Tissue Factor Precursor
Chain: U
Fragment: Factor III, Residues 123-242
Synonym: Tissue Factor, Tf, Coagulation Factor III Thromboplastin, Cd142 Antigen

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.2285 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.993 81.302 125.860 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.72 Å
ligand CA, CGU, FUC, GIL, GLC, NAG enzyme Hydrolase E.C.3.4.21.21 BRENDA
Primary referenceThe discovery of fluoropyridine-based inhibitors of the factor VIIa/TF complex--Part 2., Kohrt JT, Filipski KJ, Cody WL, Cai C, Dudley DA, Van Huis CA, Willardsen JA, Narasimhan LS, Zhang E, Rapundalo ST, Saiya-Cork K, Leadley RJ, Edmunds JJ, Bioorg Med Chem Lett. 2006 Feb 15;16(4):1060-4. Epub 2005 Nov 11. PMID:16289811
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (2c4f.pdb1.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 2C4F
  • CSU: Contacts of Structural Units for 2C4F
  • Likely Quarternary Molecular Structure file(s) for 2C4F
  • Structure Factors (710 Kb)
  • Retrieve 2C4F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2C4F from S2C, [Save to disk]
  • Re-refined 2c4f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2C4F 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 2C4F
  • 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 2C4F, from MSDmotif at EBI
  • Fold representative 2c4f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2c4f] [2c4f_L] [2c4f_T] [2c4f_U] [2c4f_H]
  • SWISS-PROT database: [P08709] [P13726]
  • Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM
  • Domains found in 2C4F: [EGF] [EGF_CA] [GLA] [Tryp_SPc ] by SMART
  • Other resources with information on 2C4F
  • Community annotation for 2C4F 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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