1YTM

Crystal structure of phosphoenolpyruvate carboxykinase of Anaerobiospirillum succiniciproducens complexed with ATP, oxalate, magnesium and manganese ions

Structural Biology Knowledgebase: 1YTM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.215

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YTM

Classification: LYASE

Total Structure Weight: 118773.52

Macromolecule Entities
Molecule Chains Length Organism Details
phosphoenolpyruvate carboxykinase [ATP] A, B 532 Anaerobiospirillum succiniciproducens EC#: 4.1.1.49 IUBMB
Gene Name(s): pckA

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ATP
Query on ATP

A, B ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXD
Query on OXD

A, B OXALIC ACID
C2 H2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.215
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 194.87 α = 90.00
b = 123.22 β = 90.00
c = 48.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-10
  • Released Date: 2006-01-24
  • Deposition author(s): Delbaere, L.T.J., Cotelesage, J.J.H.

Revision History

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