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(-) Description

Title :  CRYSTAL STRUCTURE OF PIRATOXIN I (A MYOTOXIC LYS49-PLA2) COMPLEXED WITH ALPHA-TOCOPHEROL
 
Authors :  J. I. Dos Santos, M. R. M. Fontes
Date :  25 Apr 08  (Deposition) - 05 May 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lys49-Pla2, Bothrops Pirajai, Sanke Venom, X-Ray Crystallography, Alpha-Tocopherol, Prtx-I, Myotoxin, Secreted, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Dos Santos, A. M. Soares, M. R. Fontes
Comparative Structural Studies On Lys49-Phospholipases A(2) From Bothrops Genus Reveal Their Myotoxic Site.
J. Struct. Biol. V. 167 106 2009
PubMed-ID: 19401234  |  Reference-DOI: 10.1016/J.JSB.2009.04.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG 2
    Chains: A, B
    Organism Common: PIRAJA'S LANCE HEAD
    Organism Scientific: BOTHROPS PIRAJAI
    Organism Taxid: 113192
    Synonym: PIRATOXIN-II, PRTX-II

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
2SO45Ligand/IonSULFATE ION
3VIT2Ligand/IonVITAMIN E

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:33 , ARG A:34 , LYS A:53 , HOH A:365 , HOH A:466BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARELYS A:115 , ARG A:118BINDING SITE FOR RESIDUE SO4 A 303
3AC3SOFTWARETHR A:81 , ILE A:104 , ARG A:107 , HOH A:315 , HOH A:325 , LYS B:36BINDING SITE FOR RESIDUE SO4 A 305
4AC4SOFTWARELYS B:20 , THR B:59 , LYS B:115 , ARG B:118 , SO4 B:309 , HOH B:525BINDING SITE FOR RESIDUE SO4 B 308
5AC5SOFTWAREGLY B:15 , LYS B:16 , ASN B:17 , LYS B:20 , SO4 B:308 , HOH B:569BINDING SITE FOR RESIDUE SO4 B 309
6AC6SOFTWARELEU A:2 , GLY A:6 , PRO A:18 , TYR A:22 , GLY A:23 , GLY A:30 , VAL A:31 , HOH A:447 , HOH A:463 , LYS B:69 , VIT B:310 , HOH B:555BINDING SITE FOR RESIDUE VIT A 306
7AC7SOFTWAREVAL A:31 , LEU A:32 , LYS A:69 , LEU A:121 , LYS A:122 , PRO A:123 , VIT A:306 , LEU B:2 , PHE B:3 , GLY B:6 , LYS B:7 , LEU B:10 , PRO B:18 , TYR B:22 , GLY B:23 , GLY B:30 , HIS B:48 , LYS B:49 , TYR B:52BINDING SITE FOR RESIDUE VIT B 310
8AC8SOFTWAREPHE B:3 , LYS B:7 , LEU B:10 , GLN B:11 , TYR B:75 , TRP B:77 , HOH B:411 , HOH B:542 , HOH B:543 , HOH B:544 , HOH B:562BINDING SITE FOR RESIDUE PE4 B 311

(-) 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  (0, 0)

(no "Cis Peptide Bond" information available for 3CYL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CYL)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2H2_BOTPI43-50
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2H2_BOTPI85-95
 		  2A:95-105
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 3CYL)

(-) 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:121
 aligned with PA2H2_BOTPI | P82287 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H2_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 121
               SCOP domains d3cyla_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 3cylA00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyl A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129    


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2H2_BOTPI | P82287 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H2_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 121
               SCOP domains d3cylb_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 3cylB00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyl B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3CYL)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA2H2_BOTPI | P82287)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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
        PA2H2_BOTPI | P82287: 1qll 2q2j

(-) Related Entries Specified in the PDB File

1clp 1pa0 1pc9 1xxs 2q2j 3cxi