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(-) Description

Title :  X-RAY STRUCTURE OF ACIDIC PHOSPHOLIPASE A2 FROM INDIAN SAW-SCALED VIPER (ECHIS CARINATUS) WITH A POTENT PLATELET AGGREGATION INHIBITORY ACTIVITY
 
Authors :  J. Jasti, M. Paramasivam, A. Srinivasan, T. P. Singh
Date :  08 Apr 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Enzyme, Pla2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jasti, M. Paramasivam, A. Srinivasan, T. P. Singh
Structure Of An Acidic Phospholipase A2 From Indian Saw-Scaled Viper (Echis Carinatus) At 2. 6 A Resolution Reveals A Novel Intermolecular Interaction.
Acta Crystallogr. , Sect. D V. 60 66 2004
PubMed-ID: 14684894  |  Reference-DOI: 10.1107/S090744490302208X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A
    EC Number: 3.1.1.4
    Organism Common: SAW-SCALED VIPER
    Organism Scientific: ECHIS CARINATUS
    Organism Taxid: 40353
    Secretion: VENOM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , ASN A:79 , HOH A:224BINDING SITE FOR RESIDUE CA A 134

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:125
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OZ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OZ6)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2A1_ECHCA59-66  1A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A1_ECHCA101-111  1A:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1OZ6)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:120
 aligned with PA2A1_ECHCA | Q7T3S7 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:120
                                    26        36        46        56        66        76        86        96       106       116       126       136
          PA2A1_ECHCA    17 NLYQFGRMIWNRTGKLPILSYGSYGCYCGWGGQGPPKDATDRCCLVHDCCYTRVGDCSPKMTLYSYRFENGDIICDNKDPCKRAVCECDREAAICLGENVNTYDKKYKSYEDCTEEVQEC 136
               SCOP domains d1oz6a_ A: Snake phospholipase A2                                                                                        SCOP domains
               CATH domains 1oz6A00 A:1-133 Phospholipase A2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    ------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oz6 A   1 NLYQFGRMIWNRTGKLPILSYGSYGCYCGWGGQGPPKDATDRCCLVHDCCYTRVGDCSPKMTLYSYRFENGDIICDNKDPCKRAVCECDREAAICLGENVNTYDKKYKSYEDCTEEVQEC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    133
                                        14|                                      56|||                 86|                               122|   131|
                                         16                                       59||                  88                                125    133
                                                                                   61|                                                              
                                                                                    67
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OZ6)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2A1_ECHCA | Q7T3S7)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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(-) Related Entries Specified in the PDB File

1cl5 PLA2 FROM DABOIA RUSSELLI PULCHELLA