1WDK

fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)

Structural Biology Knowledgebase: 1WDK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 1WDK

Classification: LYASE OXIDOREDUCTASE / TRANSFERASE

Total Structure Weight: 242326.52

Macromolecule Entities
Molecule Chains Length Organism Details
Fatty oxidation complex alpha subunit A, B 715 Pseudomonas fragi EC#: 1.1.1.35 IUBMB 4.2.1.17 IUBMB 5.1.2.3 IUBMB 5.3.3.8 IUBMB
Gene Name(s): fadB faoA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
3-ketoacyl-CoA thiolase C, D 390 Pseudomonas fragi EC#: 2.3.1.16 IUBMB
Gene Name(s): fadA faoB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ACO
Query on ACO

C, D ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAD
Query on NAD

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
N8E
Query on N8E

A, B 3,6,9,12,15-PENTAOXATRICOSAN-1-OL
N-OCTYLPENTAOXYETHYLENE; PENTAETHYLENE GLYCOL MONOOCTYL ETHER; OCTYLPENTAGLYCOL N- OCTYLPENTAOXYETHYLENE (Synonym)
C18 H38 O6
MJELOWOAIAAUJT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HG
Query on HG

C, D MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.203
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 180.71 α = 90.00
b = 94.58 β = 111.45
c = 160.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-17
  • Released Date: 2004-07-27
  • Deposition author(s): Ishikawa, M., Tsuchiya, D., Oyama, T., Tsunaka, Y., Morikawa, K.

Revision History

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