3OMI

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with D132A mutation

Structural Biology Knowledgebase: 3OMI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3OMI

Classification: OXIDOREDUCTASE

Total Structure Weight: 187821.53

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome c oxidase, aa3 type, subunit I A, C 535 Rhodobacter sphaeroides EC#: 1.9.3.1 IUBMB
Fragment: UNP RESIDUES 17-551
Mutation: D132A
Gene Name(s): coxI RSP_1877
Cytochrome c oxidase subunit 2 B, D 256 Rhodobacter sphaeroides EC#: 1.9.3.1 IUBMB
Fragment: UNP RESIDUES 30-281
Gene Name(s): coxII RSP_1826

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

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

Protein Name: Cytochrome C Oxidase wild-type


Small Molecules
Ligands 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEA
Query on HEA

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

A, B, C, D DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE (Synonym)
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRD
Query on TRD

A, B, C, D TRIDECANE
LIPID FRAGMENT (Synonym)
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HTH
Query on HTH

B (2S,3R)-heptane-1,2,3-triol
2, (Synonym)
C7 H16 O3
HXYCHJFUBNTKQR-RQJHMYQMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

B, D CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

A, B, C, D COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU1
Query on CU1

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

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

A, C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OH
Query on OH

A, C HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.192
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 125.06 α = 90.00
b = 131.52 β = 90.00
c = 175.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-08-27
  • Released Date: 2011-02-02
  • Deposition author(s): Liu, J., Qin, L., Ferguson-Miller, S.

Revision History

  • 2014-11-19
    Type: Non-polymer description | Details: --
  • 2012-05-02
    Type: Polymer description | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4