4XDE Blood Clotting date Dec 19, 2014
title Coagulation Factor Xii Protease Domain Crystal Structure
authors M.Pathak, P.Wilmann, J.Awford, C.Li, P.M.Fisher, I.Dreveny, L.V.De J.Emsley
compound source
Molecule: Coagulation Factor Xii
Chain: A
Fragment: Protease Domain, Unp Residues 373-615
Synonym: Hageman Factor,Haf
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F12
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_cell_line: Schneider 2 (S2)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmt-Puro
symmetry Space Group: P 41 21 2
R_factor 0.222 R_Free 0.262
length a length b length c angle alpha angle beta angle gamma
124.126 124.126 38.145 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.14 Å
ligand FLC, IPA enzyme Hydrolase E.C. BRENDA

Primary referenceCoagulation Factor XII protease domain crystal structure., Pathak M, Wilmann P, Awford J, Li C, Fischer PM, Dreveny I, Dekker LV, Emsley J, J Thromb Haemost. 2015 Jan 20. doi: 10.1111/jth.12849. PMID:25604127
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (4xde.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 4XDE
  • CSU: Contacts of Structural Units for 4XDE
  • Structure Factors (300 Kb)
  • Retrieve 4XDE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4XDE from S2C, [Save to disk]
  • Re-refined 4xde structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4XDE 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 4XDE
  • 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 4XDE, from MSDmotif at EBI
  • Fold representative 4xde from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4xde_A] [4xde]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4XDE: [Tryp_SPc ] by SMART
  • Other resources with information on 4XDE
  • Community annotation for 4XDE at PDBWiki (http://pdbwiki.org)

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