1YGC Hydrolase date Jan 04, 2005
title Short Factor Viia With A Small Molecule Inhibitor
authors A.G.Olivero, C.Eigenbrot, R.Goldsmith, K.Robarge, D.R.Artis, J.Flygare, T.Rawson, C.Refino, S.Bunting, D.Kirchhofer
compound source
Molecule: Coagulation Factor Vii
Chain: H
Fragment: Heavy Chain (Residues 213-466)
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
Gene: F7
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: High Five
Expression_system_vector_type: Virus
Expression_system_plasmid: Gp67ssfvii

Molecule: Coagulation Factor Vii
Chain: L
Fragment: Light Chain, Del 1-149 From Full Length (Residues 150-212);
Synonym: Serum Prothrombin Conversion Accelerator, Spca, Proconvertin, Eptacog Alfa;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F7
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: High Five
Expression_system_vector_type: Virus
Expression_system_plasmid: Gp67ssfvii
symmetry Space Group: P 41 21 2
R_factor 0.188 R_Free 0.205
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.220 95.220 116.320 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 905, CA, SO4 BindingDB enzyme Hydrolase E.C.3.4.21.21 BRENDA
related structures by homologous chain: 1DAN, 1JBU, 1KLI
Primary referenceA selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo., Olivero AG, Eigenbrot C, Goldsmith R, Robarge K, Artis DR, Flygare J, Rawson T, Sutherlin DP, Kadkhodayan S, Beresini M, Elliott LO, DeGuzman GG, Banner DW, Ultsch M, Marzec U, Hanson SR, Refino C, Bunting S, Kirchhofer D, J Biol Chem 2005 Mar 11;280(10):9160-9. Epub 2005 Jan 4. PMID:15632123
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (1ygc.pdb1.gz) 56 Kb
  • Biological Unit Coordinates (1ygc.pdb2.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 1YGC
  • CSU: Contacts of Structural Units for 1YGC
  • Likely Quarternary Molecular Structure file(s) for 1YGC
  • Structure Factors (296 Kb)
  • Retrieve 1YGC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YGC from S2C, [Save to disk]
  • Re-refined 1ygc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YGC 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 1YGC
  • 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 1YGC, from MSDmotif at EBI
  • Fold representative 1ygc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ygc] [1ygc_L] [1ygc_H]
  • SWISS-PROT database: [P08709]
  • Domain organization of [FA7_HUMAN] by SWISSPFAM
  • Domains found in 1YGC: [EGF] [Tryp_SPc ] by SMART
  • Other resources with information on 1YGC
  • Community annotation for 1YGC 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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