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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Diaminopimelate Decarboxylase uses a Versatile Active Site for Stereospecific Decarboxylation

Levdikov, V.Blagova, L.Bose, N.Momany, C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diaminopimelate decarboxylase
A
425Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lysA
EC: 4.1.1.20
Find proteins for P00861 (Escherichia coli (strain K12))
Go to UniProtKB:  P00861
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DLY
Query on DLY

Download SDF File 
Download CCD File 
A
D-LYSINE
C6 H14 N2 O2
KDXKERNSBIXSRK-RXMQYKEDSA-N
 Ligand Interaction
LYS
Query on LYS

Download SDF File 
Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
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 = 98.997α = 90.00
b = 98.997β = 90.00
c = 176.966γ = 120.00
Software Package:
Software NamePurpose
CCP4phasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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