3NER Electron Transport date Jun 09, 2010
title Structure Of Human Type B Cytochrome B5
authors S.Terzyan, C.Zhang, M.Rivera, D.B.Benson
compound source
Molecule: Cytochrome B5 Type B
Chain: A, B
Fragment: N-Terminal Heme-Binding Domain (Unp Residues 12-1
Synonym: Cytochrome B5 Outer Mitochondrial Membrane Isoform
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cyb5b, Cyb5m, Omb5
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 1 21 1
R_factor 0.177 R_Free 0.215
length a length b length c angle alpha angle beta angle gamma
37.316 40.034 58.744 90.00 98.61 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand HEM, MG, SO4 enzyme
A, B

Primary referenceAccommodating a nonconservative internal mutation by water-mediated hydrogen bonding between beta-sheet strands: a comparison of human and rat type B (mitochondrial) cytochrome b5., Parthasarathy S, Altuve A, Terzyan S, Zhang X, Kuczera K, Rivera M, Benson DR, Biochemistry. 2011 Jun 21;50(24):5544-54. doi: 10.1021/bi2004729. Epub 2011 May, 26. PMID:21574570
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (3ner.pdb1.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 3NER
  • CSU: Contacts of Structural Units for 3NER
  • Structure Factors (221 Kb)
  • Retrieve 3NER in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NER from S2C, [Save to disk]
  • Re-refined 3ner structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NER 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 3NER
  • 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 3NER, from MSDmotif at EBI
  • Fold representative 3ner from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ner_A] [3ner_B] [3ner]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NER: [Cyt-b5 ] by SMART
  • Other resources with information on 3NER
  • Community annotation for 3NER 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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