PDB entry 6gpj

View 6gpj on RCSB PDB site
Description: Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-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: 1.94 Å
R-factor: N/A
AEROSPACI score: 0.33 (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): Domains in SCOPe 2.07: d6gpja_
  • Chain 'B':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6gpjb_
  • Chain 'C':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6gpjc_
  • 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)
      • expression tag (1)
    Domains in SCOPe 2.07: d6gpjd1, d6gpjd2
  • Heterogens: CIT, G4F, NAP, EDO, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >6gpjA (A:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlynmklhygdltdst
    clvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsvkfy
    qastselygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfnhes
    prrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndepedf
    viatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrptevdf
    lqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >6gpjB (B:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlynmklhygdltdst
    clvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsvkfy
    qastselygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfnhes
    prrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndepedf
    viatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrptevdf
    lqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >6gpjC (C:)
    rnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlynmklhygdltdst
    clvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsvkfy
    qastselygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfnhes
    prrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndepedf
    viatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrptevdf
    lqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >6gpjD (D:)
    mrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlynmklhygdltds
    tclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavktcglinsvkf
    yqastselygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfavngilfnhe
    sprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwlmlqndeped
    fviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdlkyyrptevd
    flqgdctkakqklnwkprvafdelvremvhadvelmrtnpna