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(-) Description

Title :  PORE FORMING TOXIN
 
Authors :  T. Sugawara, D. Yamashita, Y. Tanaka, I. Tanaka, M. Yao
Date :  01 Mar 14  (Deposition) - 11 Mar 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Pore Forming Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sugawara, D. Yamashita, Y. Tanaka, I. Tanaka, M. Yao
Crystal Structure Of Pore Forming Toxin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-HEMOLYSIN
    Chains: A, B, C, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SAV1163
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158878
    Strain: MU50
    Synonym: HLA

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 13)
No.NameCountTypeFull Name
1MPD13Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:176 , GLN A:177 , GLN A:194 , MET A:197 , LYS A:198 , THR A:199 , ALA A:200binding site for residue MPD A 401
02AC2SOFTWAREALA A:179 , GLY A:180 , LEU F:116 , HIS G:144 , LEU G:146binding site for residue MPD A 402
03AC3SOFTWAREHIS A:144 , GLY B:180 , SER G:114binding site for residue MPD A 403
04AC4SOFTWAREGLN B:194binding site for residue MPD B 401
05AC5SOFTWAREASN C:176 , ALA C:179 , GLN C:194 , MET C:197 , LYS C:198 , ALA C:200binding site for residue MPD C 401
06AC6SOFTWARETHR C:115 , LEU C:116 , HIS D:144 , LEU D:146 , ASN E:178 , ALA E:179 , GLY E:180binding site for residue MPD C 402
07AC7SOFTWAREASN D:176 , GLN D:194 , MET D:197 , LYS D:198binding site for residue MPD D 401
08AC8SOFTWARESER B:114 , HIS C:144 , ASN D:178 , ALA D:179 , GLY D:180binding site for residue MPD D 402
09AC9SOFTWAREASN E:176 , GLN E:177 , ALA E:179 , GLN E:194 , MET E:197 , LYS E:198binding site for residue MPD E 401
10AD1SOFTWAREASN F:176 , GLN F:194 , MET F:197 , LYS F:198binding site for residue MPD F 401
11AD2SOFTWARESER D:114 , LEU D:116 , GLY F:180binding site for residue MPD F 402
12AD3SOFTWAREASN G:176 , TYR G:182 , GLN G:194 , MET G:197 , LYS G:198 , ALA G:200binding site for residue MPD G 401
13AD4SOFTWARESER E:114 , LEU F:146 , ASN G:178 , ALA G:179 , GLY G:180binding site for residue MPD G 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P24)

(-) Cis Peptide Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1Tyr A:102 -Pro A:103
2Gly A:180 -Pro A:181
3Tyr B:102 -Pro B:103
4Gly B:180 -Pro B:181
5Tyr C:102 -Pro C:103
6Gly C:180 -Pro C:181
7Tyr D:102 -Pro D:103
8Gly D:180 -Pro D:181
9Tyr E:102 -Pro E:103
10Gly E:180 -Pro E:181
11Tyr F:102 -Pro F:103
12Gly F:180 -Pro F:181
13Tyr G:102 -Pro G:103
14Gly G:180 -Pro G:181

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P24)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P24)

(-) Exons   (0, 0)

(no "Exon" information available for 4P24)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh............eeeeeeeeee....eeeeeeeeee.......eeeeeeeeeee....eeeee....eeeeeeeeeeeeeee.......eeeeee......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.eeeee......eeeeeeee..eee..eeee.......................hhhhh.hhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p24 A   1 ADSDINIKTGTTDIGSTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNAGPYDRDSWNPVYGNQLFMKTANGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN 293
                                    10     || 21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
                                          16|                                                                                                                                                                                                                                                                                   
                                           18                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...........eeeeeeeeee....eeeeeeeeee.......eeeeeeeeeee....eeeee....eeeeeeeeeeeeeee.......eeeeee......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.eeeee......eeeeeeee..eee..eeee.......................hhhhh.hhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p24 B   1 ADSDINIKTGTTDIGTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNAGPYDRDSWNPVYGNQLFMKTANGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN 293
                                    10    ||  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
                                         15|                                                                                                                                                                                                                                                                                   
                                          18                                                                                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...........eeeeeeeeee....eeeeeeeeee.......eeeeeeeeeee....eeeeee...eeeeeeeeeeeeeee.......eeeeee......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.eeeee......eeeeeeee.................................hhhhhh.hhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p24 C   1 ADSDINIKTGTTDIGTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNAGPYDRDSWNPVYGNQLFMKTANGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN 293
                                    10    ||  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
                                         15|                                                                                                                                                                                                                                                                                   
                                          18                                                                                                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh............eeeeeeeeee....eeeeeeeeee.......eeeeeeeeeee....eeeee....eeeeeeeeeeeeeee.......eeeeee......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.eeeee......eeeeeeee..eee..eeee.......................hhhhh.hhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p24 D   1 ADSDINIKTGTTDIGNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNAGPYDRDSWNPVYGNQLFMKTANGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN 293
                                    10    ||  21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
                                         15|                                                                                                                                                                                                                                                                                    
                                          17                                                                                                                                                                                                                                                                                    


Chain E from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...........eeeeeeeeee....eeeeeeeeee.......eeeeeeeeeee....eeeeee...eeeeeeeeeeeeeee.......eeeeee......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.eeeee......eeeeeeee..eee..eeee......................hhhhhh.hhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p24 E   1 ADSDINIKTGTTDIGTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNAGPYDRDSWNPVYGNQLFMKTANGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN 293
                                    10    ||  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
                                         15|                                                                                                                                                                                                                                                                                   
                                          18                                                                                                                                                                                                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...........eeeeeeeee....eeeeeeeeee.......eeeeeeeeeee....eeeee....eeeeeeeeeeeeeee.......eeeeee......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.eeeee......eeeeeeee..eee..eeee.............................hhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p24 F   1 ADSDINIKTGTTDIGTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNAGPYDRDSWNPVYGNQLFMKTANGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN 293
                                    10    ||  23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
                                         15|                                                                                                                                                                                                                                                                                  
                                          19                                                                                                                                                                                                                                                                                  


Chain G from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.............eeeeeeeee....eeeeeeeeee.......eeeeeee..ee....eeeeee...eeeeeeeeeeeeeee.......eeeeee......eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.eeeeee.....eeeeeeee..eee..eeee.......................hhhhh.hhhhhhhhhhh.....eeeeeee.......eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeeeeee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p24 G   1 ADSDINIKTGTTDIGSTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNAGPYDRDSWNPVYGNQLFMKTANGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN 293
                                    10     || 21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
                                          16|                                                                                                                                                                                                                                                                                   
                                           18
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4P24)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P24)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P24)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4P24)

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    Gly D:180 - Pro D:181   [ RasMol ]  
    Gly E:180 - Pro E:181   [ RasMol ]  
    Gly F:180 - Pro F:181   [ RasMol ]  
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    Tyr A:102 - Pro A:103   [ RasMol ]  
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 Related Entries

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(-) Related Entries Specified in the PDB File

4p1x 4p1y