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 Diffractionresolution 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 referenceHigh 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 (342 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.
  • 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] [2fir_C] [2fir_T] [2fir_H] [2fir_L]
  • SWISS-PROT database: [P08709] [P13726]
  • Domain organization of [FA7_HUMAN] [TF_HUMAN] by SWISSPFAM
  • Domains found in 2FIR: [EGF] [EGF_CA] [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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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