PDB entry 6q94

View 6q94 on RCSB PDB site
Description: Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-Man
Class: lyase
Keywords: GDP-mannose 4, 6 dehydratase, fucosylation, Structural Genomics, Structural Genomics Consortium, SGC, Lyase
Deposited on 2018-12-17, released 2019-04-24
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-04-24, with a file datestamp of 2019-04-19.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: N/A
AEROSPACI score: 0.16 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (2-351)
      • engineered mutation (135)
    Domains in SCOPe 2.08: d6q94a_
  • Chain 'B':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (2-351)
      • engineered mutation (135)
    Domains in SCOPe 2.08: d6q94b_
  • Chain 'C':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (2-351)
      • engineered mutation (135)
    Domains in SCOPe 2.08: d6q94c_
  • Chain 'D':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (2-351)
      • engineered mutation (135)
    Domains in SCOPe 2.08: d6q94d_
  • Chain 'E':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (2-351)
      • engineered mutation (135)
    Domains in SCOPe 2.08: d6q94e_
  • Chain 'F':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (2-351)
      • engineered mutation (135)
    Domains in SCOPe 2.08: d6q94f_
  • Chain 'G':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (2-351)
      • engineered mutation (135)
    Domains in SCOPe 2.08: d6q94g_
  • Chain 'H':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (2-351)
      • engineered mutation (135)
    Domains in SCOPe 2.08: d6q94h_
  • Heterogens: NAP, GDD, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6q94A (A:)
    smrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnm
    klhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavk
    tcglinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlf
    avngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamw
    lmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvd
    lkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6q94A (A:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnmkl
    hygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktc
    glinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfav
    ngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlm
    lqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlk
    yyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6q94B (B:)
    smrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnm
    klhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavk
    tcglinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlf
    avngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamw
    lmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvd
    lkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6q94B (B:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlykngnmklhygdlt
    dstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsv
    kfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfn
    hesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndep
    edfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrpte
    vdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6q94C (C:)
    smrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnm
    klhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavk
    tcglinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlf
    avngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamw
    lmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvd
    lkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6q94C (C:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknphiegnmklhy
    gdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcgl
    insvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavng
    ilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlq
    ndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyy
    rptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6q94D (D:)
    smrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnm
    klhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavk
    tcglinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlf
    avngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamw
    lmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvd
    lkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6q94D (D:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknnmklhygdltd
    stclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsvk
    fyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfnh
    esprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndepe
    dfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrptev
    dflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >6q94E (E:)
    smrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnm
    klhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavk
    tcglinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlf
    avngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamw
    lmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvd
    lkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6q94E (E:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnmkl
    hygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktc
    glinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfav
    ngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlm
    lqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlk
    yyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6q94F (F:)
    smrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnm
    klhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavk
    tcglinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlf
    avngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamw
    lmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvd
    lkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6q94F (F:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnmkl
    hygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktc
    glinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfav
    ngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlm
    lqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlk
    yyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >6q94G (G:)
    smrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnm
    klhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavk
    tcglinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlf
    avngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamw
    lmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvd
    lkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6q94G (G:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnmkl
    hygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktc
    glinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfav
    ngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlm
    lqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlk
    yyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >6q94H (H:)
    smrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnm
    klhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavk
    tcglinsvkfyqastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlf
    avngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamw
    lmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvd
    lkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6q94H (H:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlynmklhygdltdst
    clvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsvkfy
    qastdelygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfnhes
    prrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndepedf
    viatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrptevdf
    lqgdctkakqklnwkprvafdelvremvhadvelmrtnpna