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(-) Description

Title :  CRYSTAL STRUCTURE OF ECARPHOLIN S (SER49-PLA2) COMPLEXED WITH FATTY ACID
 
Authors :  X. Zhou, T. C. Tan, S. Valiyaveettil, M. L. Go, R. M. Kini, J. Sivaraman
Date :  02 Jul 07  (Deposition) - 16 Oct 07  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Sheet, Three Helices, Protein-Ligand Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhou, T. C. Tan, S. Valiyaveettil, M. L. Go, R. M. Kini, A. Velazquez-Campoy, J. Sivaraman
Structural Characterization Of Myotoxic Ecarpholin S From Echis Carinatus Venom
Biophys. J. V. 95 3366 2008
PubMed-ID: 18586854  |  Reference-DOI: 10.1529/BIOPHYSJ.107.117747
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A, B
    EC Number: 3.1.1.4
    Organism Common: SAW-SCALED VIPER
    Organism Scientific: ECHIS CARINATUS
    Organism Taxid: 40353
    Other Details: SNAKE VENOM GLAND
    Synonym: ECARPHOLIN S/LAURIC ACID COMPLEX, PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DAO2Ligand/IonLAURIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:28 , GLY A:30 , GLY A:31 , CYS A:45 , HIS A:48 , HOH A:557BINDING SITE FOR RESIDUE DAO A 501
2AC2SOFTWAREPHE B:28 , GLY B:30 , GLY B:31 , CYS B:45 , HIS B:48 , SER B:49BINDING SITE FOR RESIDUE DAO B 502

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:126
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96
8B:27 -B:126
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:91
14B:84 -B:96

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:19 -Pro A:20
2Gly A:35 -Pro A:36
3Phe B:19 -Pro B:20
4Gly B:35 -Pro B:36

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QHD)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2HS_ECHCA43-50
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2HS_ECHCA85-95
 		  2A:95-105
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 2QHD)

(-) 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:122
 aligned with PA2HS_ECHCA | P48650 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
          PA2HS_ECHCA     1 SVVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLPDCSPKTDRYKYKRENGEIICENSTSCKKRICECDKAVAVCLRKNLNTYNKKYTYYPNFWCKGDIEKC 122
               SCOP domains d2qhda_ A: automated matches                                                                                               SCOP domains
               CATH domains 2qhdA00 A:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qhd A   1 SVVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLPDCSPKTDRYKYKRENGEIICENSTSCKKRICECDKAVAVCLRKNLNTYNKKYTYYPNFWCKGDIEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67                                                                


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with PA2HS_ECHCA | P48650 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
          PA2HS_ECHCA     1 SVVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLPDCSPKTDRYKYKRENGEIICENSTSCKKRICECDKAVAVCLRKNLNTYNKKYTYYPNFWCKGDIEKC 122
               SCOP domains d2qhdb_ B: automated matches                                                                                               SCOP domains
               CATH domains 2qhdB00 B:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qhd B   1 SVVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLPDCSPKTDRYKYKRENGEIICENSTSCKKRICECDKAVAVCLRKNLNTYNKKYTYYPNFWCKGDIEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QHD)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA2HS_ECHCA | P48650)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.
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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PA2HS_ECHCA | P48650: 2qhe 3bjw

(-) Related Entries Specified in the PDB File

2qhe 2qhg