4OD5

Substrate-bound structure of a UbiA homolog from Aeropyrum pernix K1

Structural Biology Knowledgebase: 4OD5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.301
  • R-Value Work: 0.279

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4OD5

Classification: TRANSFERASE

Total Structure Weight: 194122.22

Macromolecule Entities
Molecule Chains Length Organism Details
4-hydroxybenzoate octaprenyltransferase A, B, C..., D, E, FA, B, C, D, E, F 303 Aeropyrum pernix EC#: 2.5.1 IUBMB
Gene Name(s): ubiA APE_1570

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

A, B, C, D, E, F GERANYL S-THIOLODIPHOSPHATE
S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE (Synonym)
C10 H20 O6 P2 S
AKIXWSDUEPPMKM-JXMROGBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PHB
Query on PHB

A, B, C, D, E, F P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.301
  • R-Value Work: 0.279
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.10 α = 90.00
b = 122.83 β = 90.00
c = 423.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-01-10
  • Released Date: 2014-03-19
  • Deposition author(s): Li, W., Cheng, W.

Revision History

No revisions since initial release