PDB entry 4iyo

View 4iyo on RCSB PDB site
Description: Crystal structure of cystathionine gamma lyase from Xanthomonas oryzae pv. oryzae (XometC) in complex with E-site serine, A-site serine, A-site external aldimine structure with aminoacrylate and A-site iminopropionate intermediates
Class: lyase
Keywords: PLP DEPENDENT ENZYME, LYASE, XOCGL, IMINOPROPIONATE, SERINE, Cys-Met metabolism PLP dependent enzyme, cystathionine gamma lyase, PLP binding
Deposited on 2013-01-29, released 2014-01-29
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-05-03, with a file datestamp of 2017-04-28.
Experiment type: XRAY
Resolution: 1.8 Å
R-factor: N/A
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Cystathionine gamma-lyase-like protein
    Species: Xanthomonas oryzae pv. oryzae [TaxId:291331]
    Gene: metB, XOCGL, XOO0778
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4iyoa_
  • Chain 'B':
    Compound: Cystathionine gamma-lyase-like protein, LYS201A modified
    Species: Xanthomonas oryzae pv. oryzae [TaxId:291331]
    Gene: metB, XOCGL, XOO0778
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4iyob_
  • Chain 'C':
    Compound: Cystathionine gamma-lyase-like protein, LYS201A modified
    Species: Xanthomonas oryzae pv. oryzae [TaxId:291331]
    Gene: metB, XOCGL, XOO0778
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4iyoc_
  • Chain 'D':
    Compound: Cystathionine gamma-lyase-like protein, LYS201A modified
    Species: Xanthomonas oryzae pv. oryzae [TaxId:291331]
    Gene: metB, XOCGL, XOO0778
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4iyod_
  • Heterogens: SER, GOL, SO4, 0JO, NAK, PYR, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4iyoA (A:)
    msnrtthshdgdralslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysr
    thnptrfayercvaaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfe
    rvrrrtagldfsfvdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhgl
    ltvvdntfaspmlqrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqn
    siggvqgpfdsflalrglktlplrmrahcenalalaqwlethpaiekviypglashpqhv
    lakrqmsgfggivsivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipv
    arreqlgisdalvrlsvgiedlgdlrgdleralvnqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4iyoA (A:)
    alslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysrthnptrfayercv
    aaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfervrrrtagldfsf
    vdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhglltvvdntfaspml
    qrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqnsiggvqgpfdsfl
    alrglktlplrmrahcenalalaqwlethpaiekviypglashpqhvlakrqmsgfggiv
    sivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipvarreqlgisdalv
    rlsvgiedlgdlrgdleralv
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4iyoB (B:)
    msnrtthshdgdralslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysr
    thnptrfayercvaaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfe
    rvrrrtagldfsfvdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhgl
    ltvvdntfaspmlqrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqn
    siggvqgpfdsflalrglktlplrmrahcenalalaqwlethpaiekviypglashpqhv
    lakrqmsgfggivsivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipv
    arreqlgisdalvrlsvgiedlgdlrgdleralvnqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4iyoB (B:)
    alslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysrthnptrfayercv
    aaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfervrrrtagldfsf
    vdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhglltvvdntfaspml
    qrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqnsiggvqgpfdsfl
    alrglktlplrmrahcenalalaqwlethpaiekviypglashpqhvlakrqmsgfggiv
    sivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipvarreqlgisdalv
    rlsvgiedlgdlrgdleralv
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4iyoC (C:)
    msnrtthshdgdralslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysr
    thnptrfayercvaaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfe
    rvrrrtagldfsfvdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhgl
    ltvvdntfaspmlqrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqn
    siggvqgpfdsflalrglktlplrmrahcenalalaqwlethpaiekviypglashpqhv
    lakrqmsgfggivsivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipv
    arreqlgisdalvrlsvgiedlgdlrgdleralvnqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4iyoC (C:)
    alslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysrthnptrfayercv
    aaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfervrrrtagldfsf
    vdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhglltvvdntfaspml
    qrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqnsiggvqgpfdsfl
    alrglktlplrmrahcenalalaqwlethpaiekviypglashpqhvlakrqmsgfggiv
    sivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipvarreqlgisdalv
    rlsvgiedlgdlrgdleralv
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4iyoD (D:)
    msnrtthshdgdralslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysr
    thnptrfayercvaaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfe
    rvrrrtagldfsfvdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhgl
    ltvvdntfaspmlqrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqn
    siggvqgpfdsflalrglktlplrmrahcenalalaqwlethpaiekviypglashpqhv
    lakrqmsgfggivsivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipv
    arreqlgisdalvrlsvgiedlgdlrgdleralvnqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4iyoD (D:)
    alslatlaihggqspdpstgavmppiyatstyaqsspgehqgfeysrthnptrfayercv
    aaleggtrafafasgmaatstvmelldagshvvamddlyggtfrlfervrrrtagldfsf
    vdltdpaafkaairadtkmvwietptnpmlklvdiaaiaviarkhglltvvdntfaspml
    qrplslgadlvvhsatkylnghsdmvggiavvgdnaelaeqmaflqnsiggvqgpfdsfl
    alrglktlplrmrahcenalalaqwlethpaiekviypglashpqhvlakrqmsgfggiv
    sivlkggfdaakrfcektelftlaeslggveslvnhpavmthasipvarreqlgisdalv
    rlsvgiedlgdlrgdleralvnqn