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(-) Description

Title :  CRYSTAL STRUCTURE OF BOTHROPS ASPER MYOTOXIN II COMPLEXED WITH THE ANTI-TRYPANOSOMAL DRUG SURAMIN
 
Authors :  M. T. Murakami, E. Z. Arruda, P. A. Melo, A. B. Martinez, S. Calil-Elias, M. A. Tomaz, B. Lomonte, J. M. Gutierrez, R. K. Arni
Date :  01 Dec 04  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bothrops Asper Myotoxin Ii, Anti-Trypanosomal Drug Suramin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Murakami, E. Z. Arruda, P. A. Melo, A. B. Martinez, S. Calil-Elias M. A. Tomaz, B. Lomonte, J. M. Gutierrez, R. K. Arni
Inhibition Of Myotoxic Activity Of Bothrops Asper Myotoxin Ii By The Anti-Trypanosomal Drug Suramin.
J. Mol. Biol. V. 350 416 2005
PubMed-ID: 15961104  |  Reference-DOI: 10.1016/J.JMB.2005.04.072

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG 2
    Chains: A, B
    EC Number: 3.1.1.4
    Organism Common: TERCIOPELO
    Organism Scientific: BOTHROPS ASPER
    Organism Taxid: 8722
    Secretion: SNAKE VENOM
    Synonym: MYOTOXIN 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
1IPA5Ligand/IonISOPROPYL ALCOHOL
2P332Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
3SVR1Ligand/Ion8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:2 , GLY A:30 , VAL A:31 , LEU A:32 , GLY A:33 , ARG A:34 , LYS A:49 , TYR A:52 , LYS A:53 , PRO A:68 , LYS A:69 , LYS A:70 , P33 A:401 , HOH A:525 , LEU B:2 , LEU B:5 , GLY B:30 , VAL B:31 , ARG B:34 , HIS B:48 , LYS B:49 , TYR B:52 , LYS B:53 , LYS B:69 , LYS B:70 , LYS B:93 , P33 B:402BINDING SITE FOR RESIDUE SVR B 301
2AC2SOFTWARELEU A:2 , GLY A:6 , LYS A:7 , LEU A:10 , PRO A:17 , TYR A:22 , ASN A:28 , CYS A:29 , GLY A:30 , CYS A:45 , HIS A:48 , LYS A:49 , SVR B:301BINDING SITE FOR RESIDUE P33 A 401
3AC3SOFTWARELEU B:2 , GLY B:6 , LYS B:7 , LEU B:10 , PRO B:17 , TYR B:22 , ASN B:28 , CYS B:29 , GLY B:30 , CYS B:45 , HIS B:48 , LYS B:49 , SVR B:301BINDING SITE FOR RESIDUE P33 B 402
4AC4SOFTWAREHOH A:550 , LEU B:58 , THR B:59 , SER B:90 , GLU B:94BINDING SITE FOR RESIDUE IPA B 501
5AC5SOFTWAREASN B:16 , LYS B:19 , SER B:20 , IPA B:505BINDING SITE FOR RESIDUE IPA B 502
6AC6SOFTWARELYS A:19 , LYS A:115 , ARG A:118BINDING SITE FOR RESIDUE IPA A 503
7AC7SOFTWAREASN A:16 , LYS A:19 , HOH A:582 , HOH A:602BINDING SITE FOR RESIDUE IPA A 504
8AC8SOFTWARELYS B:19 , LYS B:115 , ARG B:118 , IPA B:502BINDING SITE FOR RESIDUE IPA B 505

(-) SS Bonds  (14, 14)

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
8B:27 -B:125
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 1Y4L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PA2H2_BOTAS_001 *L130FPA2H2_BOTAS  ---  ---A/BL124F
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2H2_BOTAS59-66
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2H2_BOTAS101-111
 		  2A:95-105
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1Y4L)

(-) 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_BOTAS | P24605 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2H2_BOTAS    17 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLNTYNKKYRYYLKPLCKKADAC 137
               SCOP domains d1y4la_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1y4lA00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------F------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y4l A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLNTYNKKYRYYLKPLCKKADAC 133
                                    10        20|       31        41        51 ||   ||69        79    ||  90       100       110       120    || 132 
                                              20|                             53|  61|               84|                                    125|     
                                               22                              57   67                86                                     128     


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2H2_BOTAS | P24605 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2H2_BOTAS    17 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLNTYNKKYRYYLKPLCKKADAC 137
               SCOP domains d1y4lb_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1y4lB00 B:1-133 Phospholipase A2                                                                                          CATH domains
           Pfam domains (1) Phospholip_A2_1-1y4lB01 B:1-133                                                                                           Pfam domains (1)
           Pfam domains (2) Phospholip_A2_1-1y4lB02 B:1-133                                                                                           Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------F------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y4l B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLNTYNKKYRYYLKPLCKKADAC 133
                                    10        20|       31        41        51 ||   ||69        79    ||  90       100       110       120    || 132 
                                              20|                             53|  61|               84|                                    125|     
                                               22                              57   67                86                                     128
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Phospholip_A2_1] (33)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA2H2_BOTAS | P24605)
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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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

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        PA2H2_BOTAS | P24605: 1clp

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1clp