3DTU

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides complexed with deoxycholic acid

Structural Biology Knowledgebase: 3DTU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.184

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DTU

Classification: OXIDOREDUCTASE

Total Structure Weight: 198954.91

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome c oxidase subunit 1 A, C 566 Rhodobacter sphaeroides EC#: 1.9.3.1 IUBMB
Gene Name(s): ctaD
Cytochrome c oxidase subunit 2 B, D 262 Rhodobacter sphaeroides EC#: 1.9.3.1 IUBMB
Fragment: UNP residues 26-281
Gene Name(s): ctaC coxII ctaB

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)
DXC
Query on DXC

C (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN- 24-OIC ACID
DEOXYCHOLIC ACID (Synonym)
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-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)
HTO
Query on HTO

B HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-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)
PO4
Query on PO4

A, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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)
CA
Query on CA

A, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
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: 0.212
  • R-Value Work: 0.184
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 123.24 α = 90.00
b = 132.05 β = 90.00
c = 167.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-15
  • Released Date: 2008-09-16
  • Deposition author(s): Qin, L., Mills, D.A., Buhrow, L., Hiser, C., Ferguson-Miller, S.

Revision History

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