1ON9

Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with hydrolyzed methylmalonyl-coenzyme a bound)

Structural Biology Knowledgebase: 1ON9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.152

Literature

Macromolecules
Sequence Display for 1ON9

Classification: TRANSFERASE

Total Structure Weight: 343629.53

Macromolecule Entities
Molecule Chains Length Organism Details
Methylmalonyl-CoA carboxyltransferase 12S subunit A, B, C..., D, E, FA, B, C, D, E, F 523 Propionibacterium freudenreichii EC#: 2.1.3.1 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F METHYLMALONYL-COENZYME A
C25 H40 N7 O19 P3 S
MZFOKIKEPGUZEN-AGCMQPJKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

F (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A, B, C CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.152
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 113.81 α = 90.00
b = 200.02 β = 102.97
c = 145.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-27
  • Released Date: 2003-05-20
  • Deposition author(s): Hall, P.R., Wang, Y.-F., Rivera-Hainaj, R.E., Zheng, X., Pustai-Carey, M., Carey, P.R., Yee, V.C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values