1KNW Lyase date Dec 19, 2001
title Crystal Structure Of Diaminopimelate Decarboxylase
authors V.Levdikov, L.Blagova, N.Bose, C.Momany
compound source
Molecule: Diaminopimelate Decarboxylase
Chain: A
Synonym: Dap Decarboxylase
Ec: 4.1.1.20
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Lysa
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: P 61 2 2
R_factor 0.173 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.580 98.580 176.950 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand LI, MES, PLP, SO4 enzyme Lyase E.C.4.1.1.20 BRENDA
related structures by homologous chain: 1KO0
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (1knw.pdb1.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 1KNW
  • CSU: Contacts of Structural Units for 1KNW
  • Likely Quarternary Molecular Structure file(s) for 1KNW
  • Retrieve 1KNW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KNW from S2C, [Save to disk]
  • View 1KNW 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 1KNW
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1KNW, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1knwa1, region A:2-31,A:279-422 [Jmol] [rasmolscript] [script source]
        - Domain d1knwa2, region A:32-278 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1knw] [1knw_A]
  • SWISS-PROT database: [P00861]
  • Domain organization of [DCDA_ECOLI] by SWISSPFAM
  • Other resources with information on 1KNW
  • Community annotation for 1KNW 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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