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(-) Description

Title :  VOLVATOXIN A2 (DIAMOND CRYSTAL FORM)
 
Authors :  S. -C. Lin, Y. -C. Lo, J. -Y. Lin, Y. -C. Liaw
Date :  24 Apr 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Toxin, Pore Formation, Fungus, Cardiotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. -C. Lin, Y. -C. Lo, J. -Y. Lin, Y. -C. Liaw
Crystal Structures And Electron Micrographs Of Fungal Volvatoxin A2
J. Mol. Biol. V. 343 477 2004
PubMed-ID: 15451675  |  Reference-DOI: 10.1016/J.JMB.2004.08.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VOLVATOXIN A2
    Chains: A, B
    Organism Scientific: VOLVARIELLA VOLVACEA
    Organism Taxid: 36659

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:1163 , GLU B:1164 , GLU B:1165 , GLY B:1168BINDING SITE FOR RESIDUE ACT B 3001
2AC2SOFTWARELYS B:1047 , ASP B:1051BINDING SITE FOR RESIDUE ACT B 3002
3AC3SOFTWARELYS A:47 , ASP A:51BINDING SITE FOR RESIDUE ACT A 3003
4AC4SOFTWAREGLU A:164 , GLU A:165BINDING SITE FOR RESIDUE ACT A 3004
5AC5SOFTWAREALA B:1146 , PRO B:1147 , SER B:1148 , TYR B:1149BINDING SITE FOR RESIDUE ACT B 3005
6AC6SOFTWAREASP A:61 , LYS A:62 , PHE A:90 , ALA A:91 , GLU A:188BINDING SITE FOR RESIDUE ACT A 3006
7AC7SOFTWAREGLN A:23 , LYS A:26 , GLU B:1111 , TRP B:1170BINDING SITE FOR RESIDUE ACT B 3007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VGF)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VGF)

(-) Exons   (0, 0)

(no "Exon" information available for 1VGF)

(-) Sequences/Alignments

Asymmetric 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:194
 aligned with Q6USC4_9AGAR | Q6USC4 from UniProtKB/TrEMBL  Length:217

    Alignment length:194
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
        Q6USC4_9AGAR     23 NVFQPVDQLPEDLIPSSIQVLKFSGKYLKLEQDKAYFDWPGFKTAIDNYTGEDLSFDKYDQSTINQQSQEVGAMVDKIAKFLHDAFAAVVDLSKLAAIILNTFTNLEEESSSGFLQFNTNNVKKNSSWEYRVLFSVPFGDNAPSYFYSLVTTILITADIEEKTGWWGLTSSTKKNFAVQIDALELVVKKGFKAP  216
               SCOP domains d1vgfa_ A: Volvatoxin A2                                                                                                                                                                           SCOP domains
               CATH domains 1vgfA00 A:5-198 Delta-endotoxin Cytb                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeeeeeee.......eeeeeeeeeeeee...hhhhhh......eeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1vgf A    5 NVFQPVDQLPEDLIPSSIQVLKFSGKYLKLEQDKAYFDWPGFKTAIDNYTGEDLSFDKYDQSTINQQSQEVGAMVDKIAKFLHDAFAAVVDLSKLAAIILNTFTNLEEESSSGFLQFNTNNVKKNSSWEYRVLFSVPFGDNAPSYFYSLVTTILITADIEEKTGWWGLTSSTKKNFAVQIDALELVVKKGFKAP  198
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with Q6USC4_9AGAR | Q6USC4 from UniProtKB/TrEMBL  Length:217

    Alignment length:194
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
        Q6USC4_9AGAR     23 NVFQPVDQLPEDLIPSSIQVLKFSGKYLKLEQDKAYFDWPGFKTAIDNYTGEDLSFDKYDQSTINQQSQEVGAMVDKIAKFLHDAFAAVVDLSKLAAIILNTFTNLEEESSSGFLQFNTNNVKKNSSWEYRVLFSVPFGDNAPSYFYSLVTTILITADIEEKTGWWGLTSSTKKNFAVQIDALELVVKKGFKAP  216
               SCOP domains d1vgfb_ B: Volvatoxin A2                                                                                                                                                                           SCOP domains
               CATH domains 1vgfB00 B:1005-1198 Delta-endotoxin Cytb                                                                                                                                                           CATH domains
           Pfam domains (1) ----------------------------Bac_thur_toxin-1vgfB01 B:1033-1193                                                                                                                               ----- Pfam domains (1)
           Pfam domains (2) ----------------------------Bac_thur_toxin-1vgfB02 B:1033-1193                                                                                                                               ----- Pfam domains (2)
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhhh....eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeee......eeeeeeeeeeee.......eeeeeeeeeeeee...hhhhhh......eeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1vgf B 1005 NVFQPVDQLPEDLIPSSIQVLKFSGKYLKLEQDKAYFDWPGFKTAIDNYTGEDLSFDKYDQSTINQQSQEVGAMVDKIAKFLHDAFAAVVDLSKLAAIILNTFTNLEEESSSGFLQFNTNNVKKNSSWEYRVLFSVPFGDNAPSYFYSLVTTILITADIEEKTGWWGLTSSTKKNFAVQIDALELVVKKGFKAP 1198
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Bac_thur_toxin] (5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6USC4_9AGAR | Q6USC4)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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/TrEMBL
        Q6USC4_9AGAR | Q6USC4: 1pp0 1pp6 1vcy

(-) Related Entries Specified in the PDB File

1pp0 VOLVATOXIN A2 (INGOT CRYSTAL FORM)
1pp6 VOLVATOXIN A2 (STRIP CRYSTAL FORM)
1vcy VOLVATOXIN A2 ISOFORM