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 Diffraction	resolution	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
Gene Ontology	Chain Function Process Component H L
Primary reference	A 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

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 1YGC, from MSDmotif at EBI

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)

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