PDB entry 5in4

View 5in4 on RCSB PDB site
Description: Crystal Structure of GDP-mannose 4,6 dehydratase bound to a GDP-fucose based inhibitor
Class: lyase/inhibitor
Keywords: GDP-mannose 4, 6 dehydratase, antibody fucosylation, LYASE-INHIBITOR complex
Deposited on 2016-03-07, released 2016-08-17
The last revision prior to the SCOPe 2.06 freeze date was dated 2016-08-17, with a file datestamp of 2016-08-12.
Experiment type: XRAY
Resolution: 1.6 Å
R-factor: N/A
AEROSPACI score: 0.44 (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 (14-363)
      • expression tag (9-13)
    Domains in SCOPe 2.06: d5in4a1, d5in4a2
  • Chain 'B':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (14-363)
      • expression tag (13)
    Domains in SCOPe 2.06: d5in4b1, d5in4b2
  • Chain 'C':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (14-363)
      • expression tag (13)
    Domains in SCOPe 2.06: d5in4c1, d5in4c2
  • Chain 'D':
    Compound: GDP-mannose 4,6 dehydratase
    Species: Homo sapiens [TaxId:9606]
    Gene: GMDS
    Database cross-references and differences (RAF-indexed):
    • Uniprot O60547 (14-363)
      • expression tag (13)
    Domains in SCOPe 2.06: d5in4d1, d5in4d2
  • Heterogens: NAP, GDP, 6CK, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5in4A (A:)
    mhhhhhhenlyfqgrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehl
    yknpqahiegnmklhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvd
    gvgtlrlldavktcglinsvkfyqastselygkvqeipqkettpfyprspygaaklyayw
    ivvnfreaynlfavngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrd
    wghakdyveamwlmlqndepedfviatgevhsvrefveksflhigktivwegknenevgr
    cketgkvhvtvdlkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrt
    npna
    

    Sequence, based on observed residues (ATOM records): (download)
    >5in4A (A:)
    lyfqgrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahie
    gnmklhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlld
    avktcglinsvkfyqastselygkvqeipqkettpfyprspygaaklyaywivvnfreay
    nlfavngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyve
    amwlmlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhv
    tvdlkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5in4B (B:)
    mhhhhhhenlyfqgrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehl
    yknpqahiegnmklhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvd
    gvgtlrlldavktcglinsvkfyqastselygkvqeipqkettpfyprspygaaklyayw
    ivvnfreaynlfavngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrd
    wghakdyveamwlmlqndepedfviatgevhsvrefveksflhigktivwegknenevgr
    cketgkvhvtvdlkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrt
    npna
    

    Sequence, based on observed residues (ATOM records): (download)
    >5in4B (B:)
    grnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnmk
    lhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavkt
    cglinsvkfyqastselygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfa
    vngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwl
    mlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdl
    kyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5in4C (C:)
    mhhhhhhenlyfqgrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehl
    yknpqahiegnmklhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvd
    gvgtlrlldavktcglinsvkfyqastselygkvqeipqkettpfyprspygaaklyayw
    ivvnfreaynlfavngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrd
    wghakdyveamwlmlqndepedfviatgevhsvrefveksflhigktivwegknenevgr
    cketgkvhvtvdlkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrt
    npna
    

    Sequence, based on observed residues (ATOM records): (download)
    >5in4C (C:)
    grnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnmk
    lhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavkt
    cglinsvkfyqastselygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfa
    vngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwl
    mlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdl
    kyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5in4D (D:)
    mhhhhhhenlyfqgrnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehl
    yknpqahiegnmklhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvd
    gvgtlrlldavktcglinsvkfyqastselygkvqeipqkettpfyprspygaaklyayw
    ivvnfreaynlfavngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrd
    wghakdyveamwlmlqndepedfviatgevhsvrefveksflhigktivwegknenevgr
    cketgkvhvtvdlkyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrt
    npna
    

    Sequence, based on observed residues (ATOM records): (download)
    >5in4D (D:)
    grnvalitgitgqdgsylaefllekgyevhgivrrsssfntgriehlyknpqahiegnmk
    lhygdltdstclvkiinevkpteiynlgaqshvkisfdlaeytadvdgvgtlrlldavkt
    cglinsvkfyqastselygkvqeipqkettpfyprspygaaklyaywivvnfreaynlfa
    vngilfnhesprrganfvtrkisrsvakiylgqlecfslgnldakrdwghakdyveamwl
    mlqndepedfviatgevhsvrefveksflhigktivwegknenevgrcketgkvhvtvdl
    kyyrptevdflqgdctkakqklnwkprvafdelvremvhadvelmrtnpna