PDB entry 6gpk

View 6gpk on RCSB PDB site
Description: Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex with GDP-Man
Class: lyase
Keywords: GDP-mannose 4, 6 dehydratase, fucosylation, Structural Genomics, Structural Genomics Consortium, SGC, Lyase
Deposited on 2018-06-06, released 2018-07-18
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-07-18, with a file datestamp of 2018-07-13.
Experiment type: XRAY
Resolution: 1.47 Å
R-factor: N/A
AEROSPACI score: 0.49 (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 (23-372)
      • engineered mutation (157)
    Domains in SCOPe 2.07: d6gpka_
  • Chain 'B':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (23-372)
      • engineered mutation (157)
    Domains in SCOPe 2.07: d6gpkb_
  • Chain 'C':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (23-372)
      • engineered mutation (157)
    Domains in SCOPe 2.07: d6gpkc_
  • Chain 'D':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (23-372)
      • engineered mutation (157)
    Domains in SCOPe 2.07: d6gpkd_
  • Heterogens: EDO, NAP, GDD, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6gpkA (A:)
    mhhhhhhssgvdlgtenlyfqsmrnvalitgitgqdgsylaefllekgyevhgivrrsss
    fntgriehlyknpqahiegnmklhygdltdstclvkiinevkpteiynlgaqshvkisfd
    laeytadvdgvgtlrlldavktcglinsvkfyqastsqlygkvqeipqkettpfyprspy
    gaaklyaywivvnfreaynlfavngilfnhesprrganfvtrkisrsvakiylgqlecfs
    lgnldakrdwghakdyveamwlmlqndepedfviatgevhsvrefveksflhigktivwe
    gknenevgrcketgkvhvtvdlkyyrptevdflqgdctkakqklnwkprvafdelvremv
    hadvelmrtnpna
    

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

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6gpkB (B:)
    mhhhhhhssgvdlgtenlyfqsmrnvalitgitgqdgsylaefllekgyevhgivrrsss
    fntgriehlyknpqahiegnmklhygdltdstclvkiinevkpteiynlgaqshvkisfd
    laeytadvdgvgtlrlldavktcglinsvkfyqastsqlygkvqeipqkettpfyprspy
    gaaklyaywivvnfreaynlfavngilfnhesprrganfvtrkisrsvakiylgqlecfs
    lgnldakrdwghakdyveamwlmlqndepedfviatgevhsvrefveksflhigktivwe
    gknenevgrcketgkvhvtvdlkyyrptevdflqgdctkakqklnwkprvafdelvremv
    hadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6gpkB (B:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnmkl
    hygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktc
    glinsvkfyqastsqlygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfav
    ngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlm
    lqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlk
    yyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6gpkC (C:)
    mhhhhhhssgvdlgtenlyfqsmrnvalitgitgqdgsylaefllekgyevhgivrrsss
    fntgriehlyknpqahiegnmklhygdltdstclvkiinevkpteiynlgaqshvkisfd
    laeytadvdgvgtlrlldavktcglinsvkfyqastsqlygkvqeipqkettpfyprspy
    gaaklyaywivvnfreaynlfavngilfnhesprrganfvtrkisrsvakiylgqlecfs
    lgnldakrdwghakdyveamwlmlqndepedfviatgevhsvrefveksflhigktivwe
    gknenevgrcketgkvhvtvdlkyyrptevdflqgdctkakqklnwkprvafdelvremv
    hadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6gpkC (C:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlygnmklhygdltds
    tclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsvkf
    yqastsqlygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfnhe
    sprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndeped
    fviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrptevd
    flqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6gpkD (D:)
    mhhhhhhssgvdlgtenlyfqsmrnvalitgitgqdgsylaefllekgyevhgivrrsss
    fntgriehlyknpqahiegnmklhygdltdstclvkiinevkpteiynlgaqshvkisfd
    laeytadvdgvgtlrlldavktcglinsvkfyqastsqlygkvqeipqkettpfyprspy
    gaaklyaywivvnfreaynlfavngilfnhesprrganfvtrkisrsvakiylgqlecfs
    lgnldakrdwghakdyveamwlmlqndepedfviatgevhsvrefveksflhigktivwe
    gknenevgrcketgkvhvtvdlkyyrptevdflqgdctkakqklnwkprvafdelvremv
    hadvelmrtnpna
    

    Sequence, based on observed residues (ATOM records): (download)
    >6gpkD (D:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlykngnmklhygdlt
    dstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsv
    kfyqastsqlygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfn
    hesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndep
    edfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrpte
    vdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna