1KO0

Crystal Structure of a D,L-lysine complex of diaminopimelate decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 1KO0

Classification: LYASE

Total Structure Weight: 47461.34

Macromolecule Entities
Molecule Chains Length Organism Details
Diaminopimelate decarboxylase A 425 Escherichia coli EC#: 4.1.1.20 IUBMB
Gene Name(s): lysA b2838 JW2806
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LYS
Query on LYS

A LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DLY
Query on DLY

A D-LYSINE
C6 H14 N2 O2
KDXKERNSBIXSRK-RXMQYKEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.181
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 99.00 α = 90.00
b = 99.00 β = 90.00
c = 176.97 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-19
  • Released Date: 2003-11-11
  • Deposition author(s): Levdikov, V., Blagova, L., Bose, N., Momany, C.

Revision History

  • Version 1_0: 2003-11-11

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance