1M56

Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type)

Structural Biology Knowledgebase: 1M56 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.236

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1M56

Classification: OXIDOREDUCTASE

Total Structure Weight: 269275.16

Macromolecule Entities
Molecule Chains Length Organism Details
CYTOCHROME C OXIDASE A, G 566 Rhodobacter sphaeroides EC#: 1.9.3.1 IUBMB
Mutation: S436I, T437Y, S438F, G439W, S518T, S520T
Gene Name(s): ctaD
CYTOCHROME C OXIDASE B, H 264 Rhodobacter sphaeroides EC#: 1.9.3.1 IUBMB
Gene Name(s): ctaC coxII ctaB
CYTOCHROME C OXIDASE C, I 266 Rhodobacter sphaeroides EC#: 1.9.3.1 IUBMB
Mutation: N30F, I92M, M244I
Gene Name(s):
CYTOCHROME C OXIDASE D, J 51 Rhodobacter sphaeroides EC#: 1.9.3.1 IUBMB
Gene Name(s): coxIV

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

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

Protein Name: Cytochrome C Oxidase wild-type


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

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

A, C, D, G, I, J DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

A, B, G, H COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, G CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, G MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.236
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 340.36 α = 90.00
b = 340.36 β = 90.00
c = 89.67 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-08
  • Released Date: 2002-08-28
  • Deposition author(s): Svensson-Ek, M., Abramson, J., Larsson, G., Tornroth, S., Brezezinski, P., Iwata, S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4