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 Diffraction	resolution	1.72 Å
ligand	CA, CGU, FUC, GIL, GLC, NAG	enzyme	Hydrolase E.C.3.4.21.21 BRENDA
Primary reference	The 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_H] [2c4f_L] [2c4f_T] [2c4f_U] SWISS-PROT database: [P08709] [P13726] Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM Domains found in 2C4F: [EGF_CA] [EGF_like] [GLA] [Tryp_SPc ] by SMART Alignments of the sequence of 2C4F with the sequences similar proteins can be viewed for 2C4F'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 2C4F

Community annotation for 2C4F at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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