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 2.08 freeze date was dated 2019-04-24, with a file datestamp of 2019-04-19.
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 2.08: 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 2.08: 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 2.08: 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 2.08: 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