1KC7

Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 1KC7

Classification: TRANSFERASE

Total Structure Weight: 97217.38

Macromolecule Entities
Molecule Chains Length Organism Details
pyruvate phosphate dikinase A 873 [clostridium] symbiosum EC#: 2.7.9.1 IUBMB
Gene Name(s): ppdK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A PHOSPHONOPYRUVATE
C3 H5 O6 P
CHDDAVCOAOFSLD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PPR N/A in BindingDB
Ki: 3000 nM  BindingMOAD
Ki: 3000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.198
  • Space Group: P 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 89.21 α = 90.00
b = 58.42 β = 94.99
c = 102.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-07
  • Released Date: 2002-01-30
  • Deposition author(s): Chen, C.C., Howard, A., Herzberg, O.

Revision History

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