1QLE Oxidoreductase Immune System date Aug 30, 1999
title Cryo-Structure Of The Paracoccus Denitrificans Four-Subunit C Oxidase In The Completely Oxidized State Complexed With A Fv Fragment
authors A.Harrenga, H.Michel
compound source
Molecule: Cytochrome C Oxidase Polypeptide I-Beta
Chain: A
Synonym: Cytochrome Aa3 Subunit 1-Beta
Ec: 1.9.3.1
 Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266
Atcc: 13543
Cellular_location: Cytoplasmic Membrane

Molecule: Cytochrome C Oxidase Polypeptide II
Chain: B
Synonym: Cytochrome Aa3 Subunit 2, Oxidase Aa(3) Subunit 2
Ec: 1.9.3.1
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266
Atcc: 13543
Cellular_location: Cytoplasmic Membrane

Molecule: Cytochrome C Oxidase Polypeptide III
Chain: C
Synonym: Cytochrome Aa3subunit 3, Oxidase Aa(3) Subunit 3
Ec: 1.9.3.1
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266
Atcc: 13543
Cellular_location: Cytoplasmic Membrane

Molecule: Ccytochrome C Oxidase
Chain: D
Synonym: Cytochrome Aa3
Ec: 1.9.3.1
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266
Atcc: 13543
Cellular_location: Cytoplasmic Membrane

Molecule: Heavy Chain Antibody Fv Fragment
Chain: H
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Light Chain Antibody Fv Fragment
Chain: L
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 4
R_factor 0.235 R_Free 0.309
crystal
cell
length a length b length c angle alpha angle beta angle gamma
205.200 205.200 81.100 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CA, CU, CUA, HEA, MN, PC1 enzyme Oxidoreductase E.C.1.9.3.1 BRENDA
note 1QLE (Molecule of the Month:pdb5)
related structures by homologous chain: 1AHW, 1AR1, 1G9E, 1M56, 1M57, 2GFB
Gene
Ontology
ChainFunctionProcessComponent
A
  • cytochrome-c oxidase activit...


    • B
  • cytochrome-c oxidase activit...


    • C
  • cytochrome-c oxidase activit...


    • Primary referenceThe cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction., Harrenga A, Michel H, J Biol Chem 1999 Nov 19;274(47):33296-9. PMID:10559205
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (227 Kb) [Save to disk]
  • Biological Unit Coordinates (1qle.pdb1.gz) 215 Kb
  • LPC: Ligand-Protein Contacts for 1QLE
  • CSU: Contacts of Structural Units for 1QLE
  • Likely Quarternary Molecular Structure file(s) for 1QLE
  • Retrieve 1QLE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QLE from S2C, [Save to disk]
    • View 1QLE 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 1QLE
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1QLE, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qlea_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1qleb2, region B:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1qleb1, region B:108-252 [Jmol] [rasmolscript] [script source]
        - Domain d1qlec_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1qled_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1qleh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1qlel_, region L [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: [1qle_L] [1qle] [1qle_B] [1qle_H] [1qle_C] [1qle_A] [1qle_D]
  • SWISS-PROT database: [P98002] [P08306] [P06030] [P77921]
  • Belongs to the proton-translocating cytochrome oxidase (cox) superfamily according to TCDB.
  • Domain organization of [COX1B_PARDE] [COX2_PARDE] [COX3_PARDE] [COX4_PARDE] by SWISSPFAM
  • Domain found in 1QLE: [IGv ] by SMART
    • Other resources with information on 1QLE
  • Community annotation for 1QLE 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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