2FIR	Hydrolase Hydrolase Inhibitor	date	Dec 30, 2005
title	Crystal Structure Of Dfpr-Viiastf
authors	S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, M.S.Bajaj, D.Prevost, H.Sc
compound		source
Molecule: Coagulation Factor Vii Light Chain Chain: L Ec: 3.4.21.21 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: F7 Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_cell_line: Bhkvp16
Molecule: Coagulation Factor Vii Heavy Chain (Ec 3.4.21.21) Chain: H Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: F7 Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_cell_line: Bhkvp16
Molecule: Tissue Factor Chain: T Synonym: Tf, Coagulation Factor III, Thromboplastin, Cd142 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: F3 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.207 R_Free 0.281
crystal cell	length a length b length c angle alpha angle beta angle gamma 70.020 80.980 126.330 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	0G7, ACL, CA, CGU, CL, DPN, FUC, GLC, MG, NA, ZN	enzyme	Hydrolase E.C.3.4.21.21 BRENDA
Primary reference	High resolution structures of p-aminobenzamidine- and benzamidine-VIIa/soluble tissue factor: Unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+ and Zn2+ sites in factor VIIa., Bajaj SP, Schmidt AE, Agah S, Bajaj MS, Padmanabhan K, J Biol Chem. 2006 Jun 6;. PMID:16757484

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (119 Kb) [Save to disk] Biological Unit Coordinates (2fir.pdb1.gz) 111 Kb LPC: Ligand-Protein Contacts for 2FIR CSU: Contacts of Structural Units for 2FIR Likely Quarternary Molecular Structure file(s) for 2FIR Structure Factors (350 Kb) Retrieve 2FIR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2FIR from S2C, [Save to disk] Re-refined 2fir structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2FIR 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 2FIR

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 2FIR, from MSDmotif at EBI Fold representative 2fir from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2fir_C] [2fir_H] [2fir_L] [2fir_T] SWISS-PROT database: [P08709] [P13726] Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM Domains found in 2FIR: [EGF_CA] [EGF_like] [GLA] [Tryp_SPc ] by SMART Alignments of the sequence of 2FIR with the sequences similar proteins can be viewed for 2FIR'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 2FIR

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

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