4GP4

Structure of Recombinant Cytochrome ba3 Oxidase mutant Y133F from Thermus thermophilus

Structural Biology Knowledgebase: 4GP4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 4GP4

Classification: OXIDOREDUCTASE

Total Structure Weight: 93202.70

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome c oxidase subunit 1 A 568 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Mutation: Y133F
Gene Name(s): cbaA TTHA1135
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c oxidase subunit 2 B 168 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Gene Name(s): cbaB ctaC TTHA1134
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c oxidase polypeptide 2A C 34 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Gene Name(s): cbaD TTHA1133
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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 6 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 NGL
 
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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLC
Query on OLC

A, B (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CUA
Query on CUA

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

A COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PER
Query on PER

A PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.179
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 144.14 α = 90.00
b = 98.58 β = 127.89
c = 94.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-20
  • Released Date: 2013-01-16
  • Deposition author(s): Li, Y., Chen, Y., Stout, C.D.
  • Previous versions: 4F05

Revision History

  • 2013-03-13
    Type: Non-polymer description | Details: --
  • 2013-02-13
    Type: Citation | Details: Citation update
  • 2013-01-23
    Type: Citation | Details: Citation update