PDB entry 4p1y

View 4p1y on RCSB PDB site
Description: Crystal structure of staphylococcal gamma-hemolysin prepore
Class: toxin
Keywords: pore forming toxin
Deposited on 2014-02-28, released 2014-10-01
The last revision prior to the SCOPe 2.08 freeze date was dated 2014-10-15, with a file datestamp of 2014-10-10.
Experiment type: XRAY
Resolution: 2.99 Å
R-factor: 0.231
AEROSPACI score: 0.16 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Gamma-hemolysin component B
    Species: Staphylococcus aureus [TaxId:158878]
    Gene: hlgB, SAV2421
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q931F3 (Start-308)
      • engineered mutation (185)
    Domains in SCOPe 2.08: d4p1ya_
  • Chain 'B':
    Compound: Gamma-hemolysin component A
    Species: Staphylococcus aureus [TaxId:158878]
    Gene: hlgA, hlg2, SAV2419
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0A071 (22-289)
      • expression tag (15-21)
    Domains in SCOPe 2.08: d4p1yb1, d4p1yb2
  • Chain 'C':
    Compound: Gamma-hemolysin component B
    Species: Staphylococcus aureus [TaxId:158878]
    Gene: hlgB, SAV2421
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q931F3 (Start-308)
      • engineered mutation (185)
      • engineered mutation (206)
    Domains in SCOPe 2.08: d4p1yc_
  • Chain 'D':
    Compound: Gamma-hemolysin component A
    Species: Staphylococcus aureus [TaxId:158878]
    Gene: hlgA, hlg2, SAV2419
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0A071 (22-289)
      • expression tag (15-21)
    Domains in SCOPe 2.08: d4p1yd1, d4p1yd2
  • Chain 'E':
    Compound: Gamma-hemolysin component B
    Species: Staphylococcus aureus [TaxId:158878]
    Gene: hlgB, SAV2421
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q931F3 (Start-308)
      • engineered mutation (185)
    Domains in SCOPe 2.08: d4p1ye_
  • Chain 'F':
    Compound: Gamma-hemolysin component A
    Species: Staphylococcus aureus [TaxId:158878]
    Gene: hlgA, hlg2, SAV2419
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0A071 (22-289)
      • expression tag (15-21)
    Domains in SCOPe 2.08: d4p1yf1, d4p1yf2
  • Chain 'G':
    Compound: Gamma-hemolysin component B
    Species: Staphylococcus aureus [TaxId:158878]
    Gene: hlgB, SAV2421
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q931F3 (Start-308)
      • engineered mutation (185)
    Domains in SCOPe 2.08: d4p1yg_
  • Chain 'H':
    Compound: Gamma-hemolysin component A
    Species: Staphylococcus aureus [TaxId:158878]
    Gene: hlgA, hlg2, SAV2419
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0A071 (22-289)
      • expression tag (15-21)
    Domains in SCOPe 2.08: d4p1yh1, d4p1yh2

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4p1yA (A:)
mghhhhhhamegkitpvsvkkvddkvtlykttatadsdkfkisqiltfnfikdksydkdt
lvlkatgninsgfvkpnpndydfsklywgakynvsissqsndsvnvvdyapknqneefqv
qntlgytfggdisisnglsgglngntafsetinykqesyrttlsrntnyknvgwgveahk
imnngagpygrdsfhptygnelflagaqssayagqnfiaqhqmpllsrsnfnpeflsvls
hrqdgakkskitvtyqremdlyqicwngfywaganyknfktrtfkstyeidwenhkvkll
dtketennk

    Sequence, based on observed residues (ATOM records): (download) 
    >4p1yA (A:)
vtlykttatadsdkfkisqiltfnfikdksydkdtlvlkatgninsgfvkpnpndydfsk
lywgakynvsissqsndsvnvvdyapknqneefqvqntlgytfgntafsetinykqesyr
ttlsrntnyknvgwgveahkimnngagpygrdsfhptygnelflagssayagqnfiaqhq
mpllsrsnfnpeflsvlshrqdgakkskitvtyqremdlyqicwngfywaganyknfktr
tfkstyeidwenhkvklldtketennk

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4p1yB (B:)
mghhhhhhamenkiedigqgaeiikrtqditskrlaitqniqfdfvkdkkynkdalvvkm
qgfissrttysdlkkypyikrmiwpfqynislktkdsnvdlinylpknkidsadvsqklg
yniggnfqsapsiggsgsfnysktisynqknyvtevesqnskgvkwgvkansfvtpngqv
saydqylfaqdptgpaardyfvpdnqlppliqsgfnpsfittlshergkgdksefeityg
rnmdatyayvtrhrlavdrkhdafknrnvtvkyevnwkthevkiksitpk

    Sequence, based on observed residues (ATOM records): (download) 
    >4p1yB (B:)
digqgaeiikrtqditskrlaitqniqfdfvkdkkynkdalvvkmqgfissrttysdlkk
ypyikrmiwpfqynislktkdsnvdlinylpknkidsadvsqklgynigsgsfnysktis
ynqknyvtevesqnskgvkwgvkansfvtpngqvsaydqylfaqdptgpaardyfvpdnq
lppliqsgfnpsfittlshergkgdksefeitygrnmdatyayvtrhrlavdrkhdafkn
rnvtvkyevnwkthevkiksitpk

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4p1yC (C:)
mghhhhhhamegkitpvsvkkvddkvtlykttatadsdkfkisqiltfnfikdksydkdt
lvlkatgninsgfvkpnpndydfsklywgakynvsissqsndsvnvvdyapknqneefqv
qntlgytfggdisisnglsgglngntafsetinykqesyrttlsrntnyknvgwgveahk
imnngagpygrdsfhptygnelflagaqssayagqnfiaqhqmpllsrsnfnpeflsvls
hrqdgakkskitvtyqremdlyqicwngfywaganyknfktrtfkstyeidwenhkvkll
dtketennk

    Sequence, based on observed residues (ATOM records): (download) 
    >4p1yC (C:)
vtlykttatadsdkfkisqiltfnfikdksydkdtlvlkatgninsgfvkpnpndydfsk
lywgakynvsissqsndsvnvvdyapknqneefqvqntlgytfgntafsetinykqesyr
ttlsrntnyknvgwgveahkimnngagpygrdsfhptygnelflagaayagqnfiaqhqm
pllsrsnfnpeflsvlshrqdgakkskitvtyqremdlyqicwngfywaganyknfktrt
fkstyeidwenhkvklldtketennk

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4p1yD (D:)
mghhhhhhamenkiedigqgaeiikrtqditskrlaitqniqfdfvkdkkynkdalvvkm
qgfissrttysdlkkypyikrmiwpfqynislktkdsnvdlinylpknkidsadvsqklg
yniggnfqsapsiggsgsfnysktisynqknyvtevesqnskgvkwgvkansfvtpngqv
saydqylfaqdptgpaardyfvpdnqlppliqsgfnpsfittlshergkgdksefeityg
rnmdatyayvtrhrlavdrkhdafknrnvtvkyevnwkthevkiksitpk

    Sequence, based on observed residues (ATOM records): (download) 
    >4p1yD (D:)
digqgaeiikrtqditskrlaitqniqfdfvkdkkynkdalvvkmqgfissrttysdlkk
ypyikrmiwpfqynislktkdsnvdlinylpknkidsadvsqklgynigsgsfnysktis
ynqknyvtevesqnskgvkwgvkansfvtpngqvsaydqylfaqdptgpaardyfvpdnq
lppliqsgfnpsfittlshergkgdksefeitygrnmdatyayvtrhrlavdrkhdafkn
rnvtvkyevnwkthevkiksitpk

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4p1yE (E:)
mghhhhhhamegkitpvsvkkvddkvtlykttatadsdkfkisqiltfnfikdksydkdt
lvlkatgninsgfvkpnpndydfsklywgakynvsissqsndsvnvvdyapknqneefqv
qntlgytfggdisisnglsgglngntafsetinykqesyrttlsrntnyknvgwgveahk
imnngagpygrdsfhptygnelflagaqssayagqnfiaqhqmpllsrsnfnpeflsvls
hrqdgakkskitvtyqremdlyqicwngfywaganyknfktrtfkstyeidwenhkvkll
dtketennk

    Sequence, based on observed residues (ATOM records): (download) 
    >4p1yE (E:)
vtlykttatadsdkfkisqiltfnfikdksydkdtlvlkatgninsgfvkpnpndydfsk
lywgakynvsissqsndsvnvvdyapknqneefqvqntlgytfgntafsetinykqesyr
ttlsrntnyknvgwgveahkimnngagpygrdsfhptygnelflagayagqnfiaqhqmp
llsrsnfnpeflsvlshrqdgakkskitvtyqremdlyqicwngfywaganyknfktrtf
kstyeidwenhkvklldtketennk

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >4p1yF (F:)
mghhhhhhamenkiedigqgaeiikrtqditskrlaitqniqfdfvkdkkynkdalvvkm
qgfissrttysdlkkypyikrmiwpfqynislktkdsnvdlinylpknkidsadvsqklg
yniggnfqsapsiggsgsfnysktisynqknyvtevesqnskgvkwgvkansfvtpngqv
saydqylfaqdptgpaardyfvpdnqlppliqsgfnpsfittlshergkgdksefeityg
rnmdatyayvtrhrlavdrkhdafknrnvtvkyevnwkthevkiksitpk

    Sequence, based on observed residues (ATOM records): (download) 
    >4p1yF (F:)
digqgaeiikrtqditskrlaitqniqfdfvkdkkynkdalvvkmqgfissrttysdlkk
ypyikrmiwpfqynislktkdsnvdlinylpknkidsadvsqklgynigsgsfnysktis
ynqknyvtevesqnskgvkwgvkansfvtpngqvsaydqylfaqdptgpaardyfvpdnq
lppliqsgfnpsfittlshergkgdksefeitygrnmdatyayvtrhrlavdrkhdafkn
rnvtvkyevnwkthevkiksitpk

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >4p1yG (G:)
mghhhhhhamegkitpvsvkkvddkvtlykttatadsdkfkisqiltfnfikdksydkdt
lvlkatgninsgfvkpnpndydfsklywgakynvsissqsndsvnvvdyapknqneefqv
qntlgytfggdisisnglsgglngntafsetinykqesyrttlsrntnyknvgwgveahk
imnngagpygrdsfhptygnelflagaqssayagqnfiaqhqmpllsrsnfnpeflsvls
hrqdgakkskitvtyqremdlyqicwngfywaganyknfktrtfkstyeidwenhkvkll
dtketennk

    Sequence, based on observed residues (ATOM records): (download) 
    >4p1yG (G:)
vtlykttatadsdkfkisqiltfnfikdksydkdtlvlkatgninsgfvkpnpndydfsk
lywgakynvsissqsndsvnvvdyapknqneefqvqntlgytfgntafsetinykqesyr
ttlsrntnyknvgwgveahkimnngagpygrdsfhptygnelflagsayagqnfiaqhqm
pllsrsnfnpeflsvlshrqdgakkskitvtyqremdlyqicwngfywaganyknfktrt
fkstyeidwenhkvklldtketennk

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >4p1yH (H:)
mghhhhhhamenkiedigqgaeiikrtqditskrlaitqniqfdfvkdkkynkdalvvkm
qgfissrttysdlkkypyikrmiwpfqynislktkdsnvdlinylpknkidsadvsqklg
yniggnfqsapsiggsgsfnysktisynqknyvtevesqnskgvkwgvkansfvtpngqv
saydqylfaqdptgpaardyfvpdnqlppliqsgfnpsfittlshergkgdksefeityg
rnmdatyayvtrhrlavdrkhdafknrnvtvkyevnwkthevkiksitpk

    Sequence, based on observed residues (ATOM records): (download) 
    >4p1yH (H:)
digqgaeiikrtqditskrlaitqniqfdfvkdkkynkdalvvkmqgfissrttysdlkk
ypyikrmiwpfqynislktkdsnvdlinylpknkidsadvsqklgynigsgsfnysktis
ynqknyvtevesqnskgvkwgvkansfvtpngqvsaydqylfaqdptgpaardyfvpdnq
lppliqsgfnpsfittlshergkgdksefeitygrnmdatyayvtrhrlavdrkhdafkn
rnvtvkyevnwkthevkiksitpk