5D6B Lyase date Aug 11, 2015
title Human Fumarase (Wild Type)
authors R.A.Pereira De Padua, M.C.Nonato
compound source
Molecule: Fumarate Hydratase, Mitochondrial
Chain: A
Fragment: Unp Residues 49-510
Synonym: Fumarase
Ec: 4.2.1.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fh
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: C 2 2 2
R_factor 0.180 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.420 147.150 57.010 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand
enzyme Lyase E.C.4.2.1.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of recombinant human fumarase., Pereira de Padua RA, Nonato MC, Acta Crystallogr F Struct Biol Commun. 2014 Jan;70(Pt 1):120-2. doi:, 10.1107/S2053230X13033955. Epub 2013 Dec 24. PMID:24419633
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (5d6b.pdb1.gz) 75 Kb
  • CSU: Contacts of Structural Units for 5D6B
  • Structure Factors (550 Kb)
  • Retrieve 5D6B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D6B from S2C, [Save to disk]
  • Re-refined 5d6b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D6B 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 5D6B
  • 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
  • Fold representative 5d6b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d6b] [5d6b_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5D6B
  • Community annotation for 5D6B at PDBWiki (http://pdbwiki.org)

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