PDB entry 6e6i

View 6e6i on RCSB PDB site
Description: Crystal structure of 4-methyl HOPDA bound to LigY from Sphingobium sp. strain SYK-6
Class: hydrolase
Keywords: C-C hydrolase, amidohydrolase superfamily, meta-cleavage, aromatic compound, HYDROLASE
Deposited on 2018-07-24, released 2019-01-30
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-01-30, with a file datestamp of 2019-01-25.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6ia_
  • Chain 'B':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6ib_
  • Chain 'C':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6ic_
  • Chain 'D':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6id_
  • Chain 'E':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6ie_
  • Chain 'F':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6if_
  • Chain 'G':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6ig_
  • Chain 'H':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6ih_
  • Chain 'I':
    Compound: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
    Species: Sphingobium sp. SYK-6 [TaxId:627192]
    Gene: ligY, SLG_07750
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6e6ii_
  • Heterogens: HVS, ZN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6e6iA (A:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6e6iB (B:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6e6iC (C:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6e6iD (D:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6e6iE (E:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6e6iF (F:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev
    

    Sequence, based on observed residues (ATOM records): (download)
    >6e6iF (F:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnle
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >6e6iG (G:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev
    

    Sequence, based on observed residues (ATOM records): (download)
    >6e6iG (G:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnle
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >6e6iH (H:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev
    

    Sequence, based on observed residues (ATOM records): (download)
    >6e6iH (H:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnle
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6e6iI (I:)
    miidchghvsapvelwaykasllahrgshgrggvkvtdeqiiaaahhketwpdghiellh
    nhgtdmqlisprpfqmmnsakparvvhwfceevntlihrqctlipemfipvaglpqvage
    pienvfaemdrcvsmgfkgfllnpdpyengaeeapplgdrywyplyeklceldlpahiha
    tgsqserspyslhfineetiatynlctssvfddfpqlkvvvshgggaipyqlgrfesqsr
    rskhlfsermaklyfdtvlytegalrllietvgperclfgsecpgvgstidpatgkqmdh
    iapfiqkfdflsdadkklifednarkvfnlev