1A3F Carboxylic Ester Hydrolase date Jan 21, 1998
title Phospholipase A2 (Pla2) From Naja Naja Venom
authors B.W.Segelke, D.Nguyen, R.Chee, H.N.Xuong, E.A.Dennis
compound source
Molecule: Phospholipase A2
Chain: A, B, C
Ec: 3.1.1.4
 Organism_scientific: Naja Naja
Organism_common: Indian Cobra
Organism_taxid: 35670
Cellular_location: Venom Sack
symmetry Space Group: P 21 21 21
R_factor 0.210 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.220 73.480 87.520 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand
enzyme Hydrolase E.C.3.1.1.4 BRENDA
related structures by homologous chain: 1GP7, 1XXW
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing., Segelke BW, Nguyen D, Chee R, Xuong NH, Dennis EA, J Mol Biol 1998 May 29;279(1):223-32. PMID:9636712
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (1a3f.pdb1.gz) 55 Kb
  • CSU: Contacts of Structural Units for 1A3F
  • Likely Quarternary Molecular Structure file(s) for 1A3F
  • Structure Factors (140 Kb)
  • Retrieve 1A3F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1A3F from S2C, [Save to disk]
  • Re-refined 1a3f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1A3F 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 1A3F
  • 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 1A3F, from MSDmotif at EBI
  • Genome occurence of 1A3F's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1a3fa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1a3fb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1a3fc_, region C [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: [1a3f_C] [1a3f_B] [1a3f_A] [1a3f]
  • SWISS-PROT database: [P15445]
  • Domain organization of [PA2_NAJNA] by SWISSPFAM
  • Domain found in 1A3F: [PA2c ] by SMART
    • Other resources with information on 1A3F
  • Community annotation for 1A3F 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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