3LF5 Oxidoreductase date Jan 15, 2010
title Structure Of Human Nadh Cytochrome B5 Oxidoreductase (Ncb5or Domain To 1.25a Resolution
authors B.Deng, S.Parthasarathy, W.Wang, B.R.Gibney, K.P.Battaile, S.Love D.R.Benson, H.Zhu
compound source
Molecule: Cytochrome B5 Reductase 4
Chain: A, B
Fragment: Unp Residues 51-137
Synonym: Flavohemoprotein B5b5r, B5+B5r, Cb5cb5r, N-Termi Cytochrome B5 And Cytochrome B5 Oxidoreductase Domain-Conta Protein;
Ec: 1.6.2.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cyb5r4, Ncb5or
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 1 21 1
R_factor 0.147 R_Free 0.173
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.480 56.370 42.560 90.00 100.67 90.00
method X-Ray Diffractionresolution 1.25 Å
ligand HEM, SO4 enzyme Oxidoreductase E.C.1.6.2.2 BRENDA
note 3LF5 is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStudy of the individual cytochrome b5 and cytochrome b5 reductase domains of Ncb5or reveals a unique heme pocket and a possible role of the CS domain., Deng B, Parthasarathy S, Wang W, Gibney BR, Battaile KP, Lovell S, Benson DR, Zhu H, J Biol Chem. 2010 Sep 24;285(39):30181-91. Epub 2010 Jul 14. PMID:20630863
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (3lf5.pdb1.gz) 72 Kb
  • Biological Unit Coordinates (3lf5.pdb2.gz) 37 Kb
  • Biological Unit Coordinates (3lf5.pdb3.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 3LF5
  • CSU: Contacts of Structural Units for 3LF5
  • Structure Factors (678 Kb)
  • Retrieve 3LF5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LF5 from S2C, [Save to disk]
  • Re-refined 3lf5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LF5 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 3LF5
  • 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
  • 3D motif for 3LF5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lf5_B] [3lf5_A] [3lf5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LF5: [Cyt-b5 ] by SMART
  • Other resources with information on 3LF5
  • Community annotation for 3LF5 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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