2EC9 Blood Clotting date Feb 13, 2007
title Crystal Structure Analysis Of Human Factor Viia , Souluble T Factor Complexed With Bcx-3607
authors K.Raman, B.Yarlagadda
compound source
Molecule: Coagulation Factor Vii
Chain: L
Fragment: Residues 1-142
Synonym: Serum Prothrombin Conversion Accelerator, Spca, Proconvertin, Eptacog Alfa;
Ec: 3.4.21.21
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bhk

Molecule: Coagulation Factor Vii
Chain: H
Fragment: Residues 16-257
Synonym: Serum Prothrombin Conversion Accelerator, Spca, Proconvertin, Eptacog Alfa;
Ec: 3.4.21.21
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bhk

Molecule: Tissue Factor
Chain: T
Fragment: Residues 38-112
Synonym: Tf, Coagulation Factor III, Thromboplastin, Cd142
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bhk

Molecule: Tissue Factor
Chain: U
Fragment: Residues 91-210
Synonym: Tf, Coagulation Factor III, Thromboplastin, Cd142
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bhk
symmetry Space Group: P 21 21 21
R_factor 0.242 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.780 81.410 125.350 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 24X, ASO, CA, CGU, FUC enzyme Hydrolase E.C.3.4.21.21 BRENDA
Primary referenceProbing the S2 site of factor VIIa to generate potent and selective inhibitors: the structure of BCX-3607 in complex with tissue factor-factor VIIa., Krishnan R, Kotian PL, Chand P, Bantia S, Rowland S, Babu YS, Acta Crystallogr D Biol Crystallogr. 2007 Jun;63(Pt 6):689-97. Epub 2007 May 15. PMID:17505107
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (2ec9.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 2EC9
  • CSU: Contacts of Structural Units for 2EC9
  • Likely Quarternary Molecular Structure file(s) for 2EC9
  • Structure Factors (372 Kb)
  • Retrieve 2EC9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2EC9 from S2C, [Save to disk]
  • Re-refined 2ec9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2EC9 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 2EC9
  • 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 2EC9, from MSDmotif at EBI
  • Fold representative 2ec9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ec9_H] [2ec9_U] [2ec9_L] [2ec9] [2ec9_T]
  • SWISS-PROT database: [P08709] [P13726]
  • Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM
  • Domains found in 2EC9: [EGF] [EGF_CA] [GLA] [Tryp_SPc ] by SMART
  • Alignments of the sequence of 2EC9 with the sequences similar proteins can be viewed for 2EC9's classification [FA7_HUMAN] [TF_HUMAN] 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 [FA7_HUMAN] [TF_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2EC9
  • Community annotation for 2EC9 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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