1D7V Lyase date Oct 19, 1999
title Crystal Structure Of The Complex Of 2,2-Dialkylglycine Decar With Nma
authors V.N.Malashkevich, M.D.Toney, P.Strop, J.Keller, J.N.Jansonius
compound source
Molecule: Protein (2,2-Dialkylglycine Decarboxylase (Pyruva
Chain: A
Synonym: Dgd
Engineered: Yes
Organism_scientific: Burkholderia Cepacia
Organism_taxid: 292
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ty103
Expression_system_plasmid: Pkdhe19
symmetry Space Group: P 64 2 2
R_factor 0.185 R_Free NULL
length a length b length c angle alpha angle beta angle gamma
153.200 153.200 86.900 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand K, NA, NMA enzyme Lyase E.C. BRENDA
related structures by homologous chain: 1DGD, 1DGE

Primary referenceCrystal structures of dialkylglycine decarboxylase inhibitor complexes., Malashkevich VN, Strop P, Keller JW, Jansonius JN, Toney MD, J Mol Biol 1999 Nov 19;294(1):193-200. PMID:10556038
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (1d7v.pdb1.gz) 261 Kb
  • LPC: Ligand-Protein Contacts for 1D7V
  • CSU: Contacts of Structural Units for 1D7V
  • Likely Quarternary Molecular Structure file(s) for 1D7V
  • Retrieve 1D7V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D7V from S2C, [Save to disk]
  • View 1D7V 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 1D7V
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1D7V, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d7va_, 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: [1d7v_A] [1d7v]
  • SWISS-PROT database: [P16932]
  • Domain organization of [DGDA_BURCE] by SWISSPFAM
  • Other resources with information on 1D7V
  • Community annotation for 1D7V 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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