1DPY Hydrolase date Dec 28, 1999
title Three-Dimensional Structure Of A Novel Phospholipase A2 From Indian Common Krait At 2.45 A Resolution
authors G.Singh, S.Gourinath, S.Sharma, M.Paramasivam, A.Srinivasan, T.P.Singh
compound source
Molecule: Phospholipase A2
Chain: A
Synonym: Pla2
Ec: 3.1.1.4
Organism_scientific: Bungarus Caeruleus
Organism_taxid: 132961
Secretion: Venom
symmetry Space Group: R 3 2
R_factor 0.202 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.980 57.980 57.980 92.02 92.02 92.02
method X-Ray Diffractionresolution 2.45 Å
ligand NA enzyme Hydrolase E.C.3.1.1.4 BRENDA
related structures by homologous chain: 1FE5, 1TD7
Gene
Ontology
ChainFunctionProcessComponent
A
  • toxin activity


  • Primary referenceSequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites., Singh G, Gourinath S, Sharma S, Paramasivam M, Srinivasan A, Singh TP, J Mol Biol 2001 Apr 6;307(4):1049-59. PMID:11286555
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (25 Kb) [Save to disk]
  • Biological Unit Coordinates (1dpy.pdb1.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 1DPY
  • CSU: Contacts of Structural Units for 1DPY
  • Likely Quarternary Molecular Structure file(s) for 1DPY
  • Retrieve 1DPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DPY from S2C, [Save to disk]
  • View 1DPY 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 1DPY
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1DPY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dpya_, 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: [1dpy_A] [1dpy]
  • SWISS-PROT database: [Q9DF52]
  • Domain organization of [PA2K_BUNCE] by SWISSPFAM
  • Domain found in 1DPY: [PA2c ] by SMART
  • Other resources with information on 1DPY
  • Community annotation for 1DPY 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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