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(-) Description

Title :  VOLVATOXIN A2 IN MONOCLINIC CRYSTAL
 
Authors :  S. -C. Lin, Y. -C. Lo, J. -Y. Lin, Y. -C. Liaw
Date :  16 Jun 03  (Deposition) - 24 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Volvatoxin A2, Ingot Crystal Form (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, C, D
    Organism Scientific: VOLVARIELLA VOLVACEA
    Organism Taxid: 36659

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric Unit (1, 13)
No.NameCountTypeFull Name
1ACY13Ligand/IonACETIC ACID
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1ACY5Ligand/IonACETIC ACID
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE D:3163 , GLU D:3164 , GLU D:3165 , HOH D:5049BINDING SITE FOR RESIDUE ACY D 4001
02AC2SOFTWARELYS B:1047 , ASP B:1051 , PHE B:1060 , HOH B:5660BINDING SITE FOR RESIDUE ACY B 4002
03AC3SOFTWARELYS A:47 , ASP A:51 , PHE A:60BINDING SITE FOR RESIDUE ACY A 4003
04AC4SOFTWAREGLN A:8 , HOH A:5043 , HOH A:5321BINDING SITE FOR RESIDUE ACY A 4004
05AC5SOFTWARETYR A:40 , ASN A:122 , SER A:131 , LEU A:158 , HOH A:5069 , HOH A:5677BINDING SITE FOR RESIDUE ACY A 4005
06AC6SOFTWARELYS C:2047 , ASP C:2051 , PHE C:2060 , HOH C:5525BINDING SITE FOR RESIDUE ACY C 4006
07AC7SOFTWAREVAL B:1093 , VAL B:1094 , ASP B:1095 , ACY B:4008BINDING SITE FOR RESIDUE ACY B 4007
08AC8SOFTWAREVAL B:1010 , ACY B:4007BINDING SITE FOR RESIDUE ACY B 4008
09AC9SOFTWARELYS D:3047 , ASP D:3051 , PHE D:3060 , HOH D:5483BINDING SITE FOR RESIDUE ACY D 4009
10BC1SOFTWAREVAL D:3010 , GLN D:3012 , HOH D:5206BINDING SITE FOR RESIDUE ACY D 4010
11BC2SOFTWAREVAL A:10 , GLN A:12 , PHE A:138 , SER A:139 , VAL A:140 , HOH A:5170BINDING SITE FOR RESIDUE ACY A 4011
12BC3SOFTWAREILE A:163 , GLU A:164 , HOH A:5100 , HOH A:5194BINDING SITE FOR RESIDUE ACY A 4012
13BC4SOFTWAREGLN D:3008 , LYS D:3098 , ILE D:3102BINDING SITE FOR RESIDUE ACY D 4013

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PP0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PP0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PP0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PP0)

(-) Exons   (0, 0)

(no "Exon" information available for 1PP0)

(-) 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:191
 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 d1pp0a_ A: Volvatoxin A2                                                                                                                                                                           SCOP domains
               CATH domains 1pp0A00 A:5-198 Delta-endotoxin Cytb                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeeeeeee.---...eeeeeeeeeeeee...hhhhhh......eeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pp0 A    5 NVFQPVDQLPEDLIPSSIQVLKFSGKYLKLEQDKAYFDWPGFKTAIDNYTGEDLSFDKYDQSTINQQSQEVGAMVDKIAKFLHDAFAAVVDLSKLAAIILNTFTNLEEESSSGFLQFNTNNVKKNSSWEYRVLFSVPF---APSYFYSLVTTILITADIEEKTGWWGLTSSTKKNFAVQIDALELVVKKGFKAP  198
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       | - |     154       164       174       184       194    
                                                                                                                                                                   142 146                                                    


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 d1pp0b_ B: Volvatoxin A2                                                                                                                                                                           SCOP domains
               CATH domains 1pp0B00 B:1005-1198 Delta-endotoxin Cytb                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeeeeeee.......eeeeeeeeeeeee...hhhhhh......eeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pp0 B 1005 NVFQPVDQLPEDLIPSSIQVLKFSGKYLKLEQDKAYFDWPGFKTAIDNYTGEDLSFDKYDQSTINQQSQEVGAMVDKIAKFLHDAFAAVVDLSKLAAIILNTFTNLEEESSSGFLQFNTNNVKKNSSWEYRVLFSVPFGDNAPSYFYSLVTTILITADIEEKTGWWGLTSSTKKNFAVQIDALELVVKKGFKAP 1198
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194    


Chain C 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 d1pp0c_ C: Volvatoxin A2                                                                                                                                                                           SCOP domains
               CATH domains 1pp0C00 C:2005-2198 Delta-endotoxin Cytb                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeeeeeee.......eeeeeeeeeeeee...hhhhhh......eeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pp0 C 2005 NVFQPVDQLPEDLIPSSIQVLKFSGKYLKLEQDKAYFDWPGFKTAIDNYTGEDLSFDKYDQSTINQQSQEVGAMVDKIAKFLHDAFAAVVDLSKLAAIILNTFTNLEEESSSGFLQFNTNNVKKNSSWEYRVLFSVPFGDNAPSYFYSLVTTILITADIEEKTGWWGLTSSTKKNFAVQIDALELVVKKGFKAP 2198
                                  2014      2024      2034      2044      2054      2064      2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174      2184      2194    


Chain D from PDB  Type:PROTEIN  Length:191
 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 d1pp0d_ D: Volvatoxin A2                                                                                                                                                                           SCOP domains
               CATH domains 1pp0D00 D:3005-3198 Delta-endotoxin Cytb                                                                                                                                                           CATH domains
           Pfam domains (1) ----------------------------Bac_thur_toxin-1pp0D01 D:3033-3193                                                                                                                               ----- Pfam domains (1)
           Pfam domains (2) ----------------------------Bac_thur_toxin-1pp0D02 D:3033-3193                                                                                                                               ----- Pfam domains (2)
           Pfam domains (3) ----------------------------Bac_thur_toxin-1pp0D03 D:3033-3193                                                                                                                               ----- Pfam domains (3)
           Pfam domains (4) ----------------------------Bac_thur_toxin-1pp0D04 D:3033-3193                                                                                                                               ----- Pfam domains (4)
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeeeeeee.---...eeeeeeeeeeeee...hhhhhh......eeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pp0 D 3005 NVFQPVDQLPEDLIPSSIQVLKFSGKYLKLEQDKAYFDWPGFKTAIDNYTGEDLSFDKYDQSTINQQSQEVGAMVDKIAKFLHDAFAAVVDLSKLAAIILNTFTNLEEESSSGFLQFNTNNVKKNSSWEYRVLFSVPF---APSYFYSLVTTILITADIEEKTGWWGLTSSTKKNFAVQIDALELVVKKGFKAP 3198
                                  3014      3024      3034      3044      3054      3064      3074      3084      3094      3104      3114      3124      3134       | - |    3154      3164      3174      3184      3194    
                                                                                                                                                                  3142   |                                                    
                                                                                                                                                                      3146
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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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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: 1pp6 1vcy 1vgf

(-) Related Entries Specified in the PDB File

1pp6 VOLVATOXIN A2 (STRIP CRYSTAL FORM)
1vcy VOLVATOXIN A2 ISOFORM
1vgf VOLVATOXIN A2 (DIAMOND CRYSTAL FORM)