1D0K Transferase date Sep 12, 1999
title The Escherichia Coli Lytic Transglycosylase Slt35 In Complex Murodipeptides (Glcnac-Murnac-L-Ala-D-Glu)
authors E.J.Van Asselt, K.H.Kalk, B.W.Dijkstra
compound source
Molecule: 35kd Soluble Lytic Transglycosylase
Chain: A
Synonym: Slt35
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.165 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.379 67.825 98.940 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.02 Å
ligand ALA, AMU, CA, DGL, GOL, NAG enzyme
related structures by homologous chain: 1D0L, 1QDR
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystallographic studies of the interactions of Escherichia coli lytic transglycosylase Slt35 with peptidoglycan., van Asselt EJ, Kalk KH, Dijkstra BW, Biochemistry 2000 Feb 29;39(8):1924-34. PMID:10684641
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1d0k.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 1D0K
  • CSU: Contacts of Structural Units for 1D0K
  • Likely Quarternary Molecular Structure file(s) for 1D0K
  • Structure Factors (166 Kb)
  • Retrieve 1D0K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D0K from S2C, [Save to disk]
  • Re-refined 1d0k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D0K in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1D0K
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1D0K, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d0ka_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1d0k] [1d0k_A]
  • SWISS-PROT database: [P41052]
  • Domain organization of [MLTB_ECOLI] by SWISSPFAM
  • Other resources with information on 1D0K
  • Community annotation for 1D0K at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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