PDB entry 5vm5

View 5vm5 on RCSB PDB site
Description: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9, with Ser bound
Class: lyase
Keywords: PLP, non-canonical amino acid, directed evolution, allostery, LYASE
Deposited on 2017-04-26, released 2017-05-24
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-09-20, with a file datestamp of 2017-09-15.
Experiment type: XRAY
Resolution: 1.67 Å
R-factor: N/A
AEROSPACI score: 0.41 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Tryptophan synthase beta chain 1
    Species: Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [TaxId:186497]
    Gene: trpB1, PF1706
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8U093 (0-End)
      • engineered mutation (15-16)
      • engineered mutation (67)
      • engineered mutation (94)
      • engineered mutation (273)
      • engineered mutation (291)
      • engineered mutation (320)
      • engineered mutation (383)
    Domains in SCOPe 2.07: d5vm5a_
  • Chain 'B':
    Compound: Tryptophan synthase beta chain 1
    Species: Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [TaxId:186497]
    Gene: trpB1, PF1706
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8U093 (0-End)
      • engineered mutation (15-16)
      • engineered mutation (67)
      • engineered mutation (94)
      • engineered mutation (273)
      • engineered mutation (291)
      • engineered mutation (320)
      • engineered mutation (383)
    Domains in SCOPe 2.07: d5vm5b_
  • Chain 'C':
    Compound: Tryptophan synthase beta chain 1
    Species: Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [TaxId:186497]
    Gene: trpB1, PF1706
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8U093 (0-End)
      • engineered mutation (15-16)
      • engineered mutation (67)
      • engineered mutation (94)
      • engineered mutation (273)
      • engineered mutation (291)
      • engineered mutation (320)
    Domains in SCOPe 2.07: d5vm5c_
  • Chain 'D':
    Compound: Tryptophan synthase beta chain 1
    Species: Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [TaxId:186497]
    Gene: trpB1, PF1706
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8U093 (0-End)
      • engineered mutation (15-16)
      • engineered mutation (67)
      • engineered mutation (94)
      • engineered mutation (273)
      • engineered mutation (291)
      • engineered mutation (320)
      • engineered mutation (383)
    Domains in SCOPe 2.07: d5vm5d_
  • Heterogens: PLS, NA, 0JO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5vm5A (A:)
    mwfgefggqyvpetlvgplkelekaykrfkddeefnrqlnyylktwagrptplyyakrlt
    ekiggakvylkredlvhggahktnnaigqallaklmgktrliaetgagqhgvatamagal
    lgmkvdiymgaedverqkmnvfrmkllganvipvnsgsrtlkdainealrdwvatfeyth
    yligsvvgphpyptivrdfqsvigreakaqileaegqlpdvivacvgggsnamgifypfv
    ndkkvklvgveaggkglesgkhsaslnagqvgvshgmlsyflqdeegqikpshsiapgld
    ypgvgpehaylkkiqraeyvavtdeealkafhelsrtegiipalesahavayamklakem
    srdeiiivnlsgrgdkdldivlkasgnvlehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vm5A (A:)
    mwfgefggqyvpetlvgplkelekaykrfkddeefnrqlnyylktwagrptplyyakrlt
    ekiggakvylkredlvhggahktnnaigqallaklmgktrliaetgagqhgvatamagal
    lgmkvdiymgaedverqkmnvfrmkllganvipvnsgsrtlkdainealrdwvatfeyth
    yligsvvgphpyptivrdfqsvigreakaqileaegqlpdvivacvgggsnamgifypfv
    ndkkvklvgveaggkglesgkhsaslnagqvgvshgmlsyflqdeegqikpshsiapgld
    ypgvgpehaylkkiqraeyvavtdeealkafhelsrtegiipalesahavayamklakem
    srdeiiivnlsgrgdkdldivlka
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5vm5B (B:)
    mwfgefggqyvpetlvgplkelekaykrfkddeefnrqlnyylktwagrptplyyakrlt
    ekiggakvylkredlvhggahktnnaigqallaklmgktrliaetgagqhgvatamagal
    lgmkvdiymgaedverqkmnvfrmkllganvipvnsgsrtlkdainealrdwvatfeyth
    yligsvvgphpyptivrdfqsvigreakaqileaegqlpdvivacvgggsnamgifypfv
    ndkkvklvgveaggkglesgkhsaslnagqvgvshgmlsyflqdeegqikpshsiapgld
    ypgvgpehaylkkiqraeyvavtdeealkafhelsrtegiipalesahavayamklakem
    srdeiiivnlsgrgdkdldivlkasgnvlehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vm5B (B:)
    mwfgefggqyvpetlvgplkelekaykrfkddeefnrqlnyylktwagrptplyyakrlt
    ekiggakvylkredlvhggahktnnaigqallaklmgktrliaetgagqhgvatamagal
    lgmkvdiymgaedverqkmnvfrmkllganvipvnsgsrtlkdainealrdwvatfeyth
    yligsvvgphpyptivrdfqsvigreakaqileaegqlpdvivacvgggsnamgifypfv
    ndkkvklvgveaggkglesgkhsaslnagqvgvshgmlsyflqgqikpshsiapgldypg
    vgpehaylkkiqraeyvavtdeealkafhelsrtegiipalesahavayamklakemsrd
    eiiivnlsgrgdkdldivlkas
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5vm5C (C:)
    mwfgefggqyvpetlvgplkelekaykrfkddeefnrqlnyylktwagrptplyyakrlt
    ekiggakvylkredlvhggahktnnaigqallaklmgktrliaetgagqhgvatamagal
    lgmkvdiymgaedverqkmnvfrmkllganvipvnsgsrtlkdainealrdwvatfeyth
    yligsvvgphpyptivrdfqsvigreakaqileaegqlpdvivacvgggsnamgifypfv
    ndkkvklvgveaggkglesgkhsaslnagqvgvshgmlsyflqdeegqikpshsiapgld
    ypgvgpehaylkkiqraeyvavtdeealkafhelsrtegiipalesahavayamklakem
    srdeiiivnlsgrgdkdldivlkasgnvlehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vm5C (C:)
    mwfgefggqyvpetlvgplkelekaykrfkddeefnrqlnyylktwagrptplyyakrlt
    ekiggakvylkredlvhggahktnnaigqallaklmgktrliaetgagqhgvatamagal
    lgmkvdiymgaedverqkmnvfrmkllganvipvnsgsrtlkdainealrdwvatfeyth
    yligsvvgphpyptivrdfqsvigreakaqileaegqlpdvivacvgggsnamgifypfv
    ndkkvklvgveaggkglesgkhsaslnagqvgvshgmlsyflqdeegqikpshsiapgld
    ypgvgpehaylkkiqraeyvavtdeealkafhelsrtegiipalesahavayamklakem
    srdeiiivnlsgrgdkdldivlk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5vm5D (D:)
    mwfgefggqyvpetlvgplkelekaykrfkddeefnrqlnyylktwagrptplyyakrlt
    ekiggakvylkredlvhggahktnnaigqallaklmgktrliaetgagqhgvatamagal
    lgmkvdiymgaedverqkmnvfrmkllganvipvnsgsrtlkdainealrdwvatfeyth
    yligsvvgphpyptivrdfqsvigreakaqileaegqlpdvivacvgggsnamgifypfv
    ndkkvklvgveaggkglesgkhsaslnagqvgvshgmlsyflqdeegqikpshsiapgld
    ypgvgpehaylkkiqraeyvavtdeealkafhelsrtegiipalesahavayamklakem
    srdeiiivnlsgrgdkdldivlkasgnvlehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vm5D (D:)
    mwfgefggqyvpetlvgplkelekaykrfkddeefnrqlnyylktwagrptplyyakrlt
    ekiggakvylkredlvhggahktnnaigqallaklmgktrliaetgagqhgvatamagal
    lgmkvdiymgaedverqkmnvfrmkllganvipvnsgsrtlkdainealrdwvatfeyth
    yligsvvgphpyptivrdfqsvigreakaqileaegqlpdvivacvgggsnamgifypfv
    ndkkvklvgveaggkglesgkhsaslnagqvgvshgmlsyflqdgqikpshsiapgldyp
    gvgpehaylkkiqraeyvavtdeealkafhelsrtegiipalesahavayamklakemsr
    deiiivnlsgrgdkdldivlkas