3QJU

The structure of and photolytic induced changes of carbon monoxide binding to the cytochrome ba3-oxidase from Thermus thermophilus

Structural Biology Knowledgebase: 3QJU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.329
  • R-Value Work: 0.286

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QJU

Classification: OXIDOREDUCTASE

Total Structure Weight: 87510.06

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome c oxidase subunit 1 A 568 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Gene Name(s): cbaA TTHA1135
Cytochrome c oxidase subunit 2 B 168 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Gene Name(s): cbaB ctaC TTHA1134
Cytochrome c oxidase polypeptide 2A C 34 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Gene Name(s): cbaD TTHA1133

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)

Protein Name: Cytochrome ba3


Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HAS
Query on HAS

A HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-QIHJKJTBDH
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CUA
Query on CUA

B DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU1
Query on CU1

A COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CMO
Query on CMO

A CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.329
  • R-Value Work: 0.286
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 109.75 α = 90.00
b = 109.75 β = 90.00
c = 164.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-30
  • Released Date: 2012-01-25
  • Deposition author(s): Liu, B., Zhang, Y., Sage, J.T., Doukov, T., Chen, Y., Stout, C.D., Fee, J.A

Revision History

  • 2012-04-04
    Type: Citation | Details: Citation update