2DKB Lyase(Decarboxylase) date Jul 12, 1994
title Dialkylglycine Decarboxylase Structure: Bifunctional Active Alkali Metal Binding Sites
authors M.D.Toney, E.Hohenester, J.N.Jansonius
compound source
Molecule: 2,2-Dialkylglycine Decarboxylase (Pyruvate)
Chain: A
Ec: 4.1.1.64
Engineered: Yes
Organism_scientific: Burkholderia Cepacia
Organism_taxid: 292
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 64 2 2
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.700 152.700 86.600 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand MES, NA, PLP enzyme Lyase E.C.4.1.1.64 BRENDA
related structures by homologous chain: 1D7S, 1M0N
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites., Toney MD, Hohenester E, Cowan SW, Jansonius JN, Science 1993 Aug 6;261(5122):756-9. PMID:8342040
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (2dkb.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (2dkb.pdb2.gz) 282 Kb
  • LPC: Ligand-Protein Contacts for 2DKB
  • CSU: Contacts of Structural Units for 2DKB
  • Likely Quarternary Molecular Structure file(s) for 2DKB
  • Retrieve 2DKB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DKB from S2C, [Save to disk]
  • View 2DKB 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 2DKB
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2DKB, from MSDmotif at EBI
  • Genome occurence of 2DKB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2dkb__, region [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: [2dkb] [2dkb_A]
  • SWISS-PROT database: [P16932]
  • Domain organization of [DGDA_BURCE] by SWISSPFAM
  • Other resources with information on 2DKB
  • Community annotation for 2DKB 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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