1M56 Oxidoreductase date Jul 08, 2002
title Structure Of Cytochrome C Oxidase From Rhodobactor Sphaeroid Type)
authors M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brezezinski,
compound source
Molecule: Cytochrome C Oxidase
Chain: A, G
Synonym: Cytochrome C Oxidase Polypeptide I
Ec: 1.9.3.1
Organism_scientific: Rhodobacter Sphaeroides
Organism_taxid: 1063

Molecule: Cytochrome C Oxidase
Chain: B, H
Synonym: Cytochrome C Oxidase Polypeptide II
Ec: 1.9.3.1

Organism_scientific: Rhodobacter Sphaeroides
Organism_taxid: 1063

Molecule: Cytochrome C Oxidase
Chain: C, I
Synonym: Cytochrome-C Oxidase Chain III
Ec: 1.9.3.1

Organism_scientific: Rhodobacter Sphaeroides
Organism_taxid: 1063

Molecule: Cytochrome C Oxidase
Chain: D, J
Ec: 1.9.3.1

Organism_scientific: Rhodobacter Sphaeroides
Organism_taxid: 1063
symmetry Space Group: H 3
R_factor 0.236 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
340.360 340.360 89.668 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand 3PE, CA, CU, HEA, MG, PEH enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
note 1M56 is a representative structure
related structures by homologous chain: 1AR1, 1M57, 1QLE
Gene
Ontology
ChainFunctionProcessComponent
A, G
  • cytochrome-c oxidase activit...


  • C, I
  • cytochrome-c oxidase activit...


  • H, B
  • cytochrome-c oxidase activit...


  • Primary referenceThe X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides., Svensson-Ek M, Abramson J, Larsson G, Tornroth S, Brzezinski P, Iwata S, J Mol Biol 2002 Aug 9;321(2):329-39. PMID:12144789
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (397 Kb) [Save to disk]
  • Biological Unit Coordinates (1m56.pdb1.gz) 191 Kb
  • Biological Unit Coordinates (1m56.pdb2.gz) 191 Kb
  • LPC: Ligand-Protein Contacts for 1M56
  • CSU: Contacts of Structural Units for 1M56
  • Likely Quarternary Molecular Structure file(s) for 1M56
  • Retrieve 1M56 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M56 from S2C, [Save to disk]
  • View 1M56 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 1M56
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1M56, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m56a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m56b1, region B:130-289 [Jmol] [rasmolscript] [script source]
        - Domain d1m56b2, region B:30-129 [Jmol] [rasmolscript] [script source]
        - Domain d1m56c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1m56d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1m56g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1m56h1, region H:130-289 [Jmol] [rasmolscript] [script source]
        - Domain d1m56h2, region H:30-129 [Jmol] [rasmolscript] [script source]
        - Domain d1m56i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1m56j_, region J [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1m56_C] [1m56_B] [1m56_J] [1m56_H] [1m56_A] [1m56_I] [1m56_G] [1m56_D] [1m56]
  • SWISS-PROT database: [P33517] [Q03736] [P84153] [Q8KRK5]
  • Belongs to the proton-translocating cytochrome oxidase (cox) superfamily according to TCDB.
  • Domain organization of [COX1_RHOSH] [COX2_RHOSH] [P84153_RHOSH] [Q8KRK5_RHOSH] by SWISSPFAM
  • Other resources with information on 1M56
  • Community annotation for 1M56 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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