3HB3

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 3HB3

Classification: OXIDOREDUCTASE

Total Structure Weight: 134103.98

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome c oxidase subunit 1-beta A 558 Paracoccus denitrificans EC#: 1.9.3.1 IUBMB
Gene Name(s): ctaDII
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c oxidase subunit 2 B 298 Paracoccus denitrificans EC#: 1.9.3.1 IUBMB
Gene Name(s): ctaC coiI ctaB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ANTIBODY FV FRAGMENT C 127 Mus musculus Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ANTIBODY FV FRAGMENT D 120 Mus musculus Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

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

Protein Name: Cytochrome C Oxidase, aa3


Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEA
Query on HEA

A HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMT
Query on LMT

A, B DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LDA
Query on LDA

A, B LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU1
Query on CU1

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

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEO
Query on PEO

A HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.218
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 83.40 α = 90.00
b = 150.47 β = 90.00
c = 157.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-05-04
  • Released Date: 2009-06-23
  • Deposition author(s): Koepke, J., Angerer, H., Peng, G.

Revision History

  • Version 1_0: 2009-06-23

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance