4BDX Hydrolase date Oct 08, 2012
title The Structure Of The Fni-Egf Tandem Domain Of Coagulation Fa
authors D.X.Beringer, L.M.J.Kroon-Batenburg
compound source
Molecule: Coagulation Factor Xiia Heavy Chain
Chain: A
Fragment: Fni-Egf, Residues 133-215
Synonym: Coagulation Factor Xii, Hageman Factor, Haf
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_strain: X-33
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppiczalpha
symmetry Space Group: I 41 2 2
R_factor 0.216 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
96.788 96.788 47.477 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.62 Å
ligand ACT enzyme Hydrolase E.C. BRENDA

Primary referenceThe structure of the FnI-EGF-like tandem domain of coagulation factor XII solved using SIRAS., Beringer DX, Kroon-Batenburg LM, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):94-102., doi: 10.1107/S1744309113000286. Epub 2013 Jan 26. PMID:23385745
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (4bdx.pdb1.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 4BDX
  • CSU: Contacts of Structural Units for 4BDX
  • Structure Factors (184 Kb)
  • Retrieve 4BDX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BDX from S2C, [Save to disk]
  • Re-refined 4bdx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BDX 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 4BDX
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4BDX, from MSDmotif at EBI
  • Fold representative 4bdx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bdx] [4bdx_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4BDX: [EGF] [FN1 ] by SMART
  • Other resources with information on 4BDX
  • Community annotation for 4BDX at PDBWiki (http://pdbwiki.org)

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