3HYW

3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 3HYW

Classification: OXIDOREDUCTASE

Total Structure Weight: 299678.22

Macromolecule Entities
Molecule Chains Length Organism Details
Sulfide-quinone reductase A, B, C..., D, E, FA, B, C, D, E, F 430 Aquifex aeolicus EC#: 1.8.5.4 IUBMB
Gene Name(s): sqr aq_2186
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Oxidoreductases

Protein Name: Sulfide:quinone oxidoreductase in complex with decylubiquinone


Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

A, B, C, D, E, F FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMT
Query on LMT

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

A, B, C, D, E, F 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5- diene-1,4-dione
decylubiquinone (Synonym)
C19 H30 O4
VMEGFMNVSYVVOM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PS9
Query on PS9

A, B, C, D, E, F octathiocane
S8
JLQNHALFVCURHW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D, E, F SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
H2S
Query on H2S

A, B, C, D, E, F HYDROSULFURIC ACID
HYDROGEN SULFIDE (Synonym)
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSS
Query on CSS
A, B, C, D, E, F L-PEPTIDE LINKING C3 H7 N O2 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.200
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 110.78 α = 90.00
b = 154.01 β = 90.00
c = 175.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-06-23
  • Released Date: 2009-07-14
  • Deposition author(s): Marcia, M., Ermler, U., Peng, G.H., Michel, H.
  • Previous versions: 3H28

Revision History

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