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(-) Description

Title :  KILLER TOXIN FROM HALOTOLERANT YEAST
 
Authors :  T. Kashiwagi, N. Kunishima, C. Suzuki, F. Tsuchiya, S. Nikkuni, Y. Arata, K. Morikawa
Date :  04 Oct 96  (Deposition) - 01 Apr 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (2x),B (2x),C (2x),D (2x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Toxin, Halotolerant Yeast (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kashiwagi, N. Kunishima, C. Suzuki, F. Tsuchiya, S. Nikkuni, Y. Arata, K. Morikawa
The Novel Acidophilic Structure Of The Killer Toxin From Halotolerant Yeast Demonstrates Remarkable Folding Similarity With A Fungal Killer Toxin.
Structure V. 5 81 1997
PubMed-ID: 9016714  |  Reference-DOI: 10.1016/S0969-2126(97)00168-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMK TOXIN
    Chains: A, C
    Fragment: CHAIN A AND C ARE RESIDUES 19 - 81 OF THE ALPHA CHAIN, CHAIN B AND D ARE RESIDUES 146 - 222 OF THE BETA CHAIN
    Organism Scientific: PICHIA FARINOSA
    Organism Taxid: 4920
    Strain: KK1
 
Molecule 2 - SMK TOXIN
    Chains: B, D
    Fragment: CHAIN A AND C ARE RESIDUES 19 - 81 OF THE ALPHA CHAIN, CHAIN B AND D ARE RESIDUES 146 - 222 OF THE BETA CHAIN
    Organism Scientific: PICHIA FARINOSA
    Organism Taxid: 4920
    Strain: KK1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE D:160 , ASP D:161 , LYS D:162 , LYS D:198 , HOH D:739BINDING SITE FOR RESIDUE SO4 D 601
2AC2SOFTWAREVAL A:67 , HIS A:70 , ASN A:71 , HOH B:810BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWAREVAL C:67 , HIS C:70 , ASN C:71 , HOH D:840BINDING SITE FOR RESIDUE SO4 C 603
4AC4SOFTWARELYS B:194 , ASN B:197 , LYS D:162BINDING SITE FOR RESIDUE SO4 B 604
5AC5SOFTWARELYS B:204 , GLY B:216 , SER B:217 , HOH B:688BINDING SITE FOR RESIDUE SO4 B 605
6AC6SOFTWARESER B:166 , LYS B:167 , HOH B:734 , SER D:217BINDING SITE FOR RESIDUE SO4 B 606
7AC7SOFTWARETRP C:19 , SER C:20 , GLY D:196 , HOH D:693BINDING SITE FOR RESIDUE SO4 C 607

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:37 -A:53
2B:190 -B:219
3C:37 -C:53
4D:190 -D:219

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KVD)

(-) 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:63
 aligned with TOXK_MILFA | P19972 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:63
                                    28        38        48        58        68        78   
           TOXK_MILFA    19 WSLRWRMQKSTTIAAIAGCSGAATFGGLAGGIVGCIAAGILAILQGFEVNWHNGGGGDRSNPV  81
               SCOP domains d1kvd.1 A:,B: SMK toxin                                         SCOP domains
               CATH domains 1kvdA00 A:19-81 Smk Toxin, alpha chain                          CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....................hhhhhhhhhhhhhhhhhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 1kvd A  19 WSLRWRMQKSTTIAAIAGCSGAATFGGLAGGIVGCIAAGILAILQGFEVNWHNGGGGDRSNPV  81
                                    28        38        48        58        68        78   


Chain B from PDB  Type:PROTEIN  Length:77
 aligned with TOXK_MILFA | P19972 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:77
                                   155       165       175       185       195       205       215       
           TOXK_MILFA   146 GEATTIWGVGADEAIDKGTPSKNDLQNMSADLAKNGFKGHQGVACSTVKDGNKDVYMIKFSLAGGSNDPGGSPCSDD 222
               SCOP domains d1kvd.1 A:,B: SMK toxin                                                       SCOP domains
               CATH domains 1kvdB00 B:146-222 Smk Toxin, beta chain                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.........hhhhhhhhhhhhhh......eeeeeeeee..eeeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 1kvd B 146 GEATTIWGVGADEAIDKGTPSKNDLQNMSADLAKNGFKGHQGVACSTVKDGNKDVYMIKFSLAGGSNDPGGSPCSDD 222
                                   155       165       175       185       195       205       215       


Chain C from PDB  Type:PROTEIN  Length:63
 aligned with TOXK_MILFA | P19972 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:63
                                    28        38        48        58        68        78   
           TOXK_MILFA    19 WSLRWRMQKSTTIAAIAGCSGAATFGGLAGGIVGCIAAGILAILQGFEVNWHNGGGGDRSNPV  81
               SCOP domains d1kvd.2 C:,D: SMK toxin                                         SCOP domains
               CATH domains 1kvdC00 C:19-81 Smk Toxin, alpha chain                          CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....................hhhhhhhhhhhhhhhhhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 1kvd C  19 WSLRWRMQKSTTIAAIAGCSGAATFGGLAGGIVGCIAAGILAILQGFEVNWHNGGGGDRSNPV  81
                                    28        38        48        58        68        78   


Chain D from PDB  Type:PROTEIN  Length:77
 aligned with TOXK_MILFA | P19972 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:77
                                   155       165       175       185       195       205       215       
           TOXK_MILFA   146 GEATTIWGVGADEAIDKGTPSKNDLQNMSADLAKNGFKGHQGVACSTVKDGNKDVYMIKFSLAGGSNDPGGSPCSDD 222
               SCOP domains d1kvd.2 C:,D: SMK toxin                                                       SCOP domains
               CATH domains 1kvdD00 D:146-222 Smk Toxin, beta chain                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.........hhhhhhhhhhhhhh......eeeeeeeee..eeeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 1kvd D 146 GEATTIWGVGADEAIDKGTPSKNDLQNMSADLAKNGFKGHQGVACSTVKDGNKDVYMIKFSLAGGSNDPGGSPCSDD 222
                                   155       165       175       185       195       205       215
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KVD)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TOXK_MILFA | P19972)
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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        TOXK_MILFA | P19972: 1kve

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