1ON3

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

Structural Biology Knowledgebase: 1ON3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.168

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1ON3

Classification: TRANSFERASE

Total Structure Weight: 344574.56

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):

Small Molecules
Ligands 4 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

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

A, B, C, D, E, F METHYLMALONIC ACID
C4 H6 O4
ZIYVHBGGAOATLY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.168
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 114.81 α = 90.00
b = 200.71 β = 102.43
c = 146.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-26
  • 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