1D0K

THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH TWO MURODIPEPTIDES (GLCNAC-MURNAC-L-ALA-D-GLU)

Structural Biology Knowledgebase: 1D0K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.165

Literature

Macromolecules
Sequence Display for 1D0K

Classification: TRANSFERASE

Total Structure Weight: 37677.55

Macromolecule Entities
Molecule Chains Length Organism Details
35KD SOLUBLE LYTIC TRANSGLYCOSYLASE A 322 Escherichia coli EC#: 4.2.2.n1 IUBMB
Mutation: L40M, L41V
Gene Name(s): mltB b2701 JW2671
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AMU
Query on AMU

A BETA-N-ACETYLMURAMIC ACID
C11 H19 N O8
MNLRQHMNZILYPY-YVNCZSHWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DGL
Query on DGL

A D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ALA
Query on ALA

A ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.165
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.38 α = 90.00
b = 67.82 β = 90.00
c = 98.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-09-12
  • Released Date: 2000-03-06
  • Deposition author(s): van Asselt, E.J., Kalk, K.H., Dijkstra, B.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update