PDB entry 7e9k

View 7e9k on RCSB PDB site
Description: crystal structure of pomgnt2 in complex with udp and mono-mannosyl peptide (379man long peptide)
Deposited on 2021-03-04, released 2021-05-05
The last revision was dated 2021-07-28, with a file datestamp of 2021-07-23.
Experiment type: XRAY
Resolution: 2.05 Å
R-factor: N/A
AEROSPACI score: 0.35 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
    Species: Bos taurus [TaxId:9913]
    Gene: POMGNT2, AGO61, GTDC2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5NDF2 (3-538)
      • expression tag (0-2)
  • Chain 'B':
    Compound: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
    Species: Bos taurus [TaxId:9913]
    Gene: POMGNT2, AGO61, GTDC2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5NDF2 (3-538)
      • expression tag (0-2)
  • Chain 'C':
    Compound: mono-mannosyl peptide (379Man long peptide)
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7E9K
  • Chain 'D':
    Compound: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
    Species: Bos taurus [TaxId:9913]
    Gene: POMGNT2, AGO61, GTDC2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5NDF2 (3-538)
      • expression tag (0-2)
  • Chain 'E':
    Compound: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
    Species: Bos taurus [TaxId:9913]
    Gene: POMGNT2, AGO61, GTDC2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5NDF2 (3-538)
      • expression tag (0-2)
  • Chain 'F':
    Compound: mono-mannosyl peptide (379Man long peptide)
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 7E9K
  • Heterogens: MAN, NH2, TRS, UDP, NAG, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >7e9kA (A:)
gappapalridypkalqilteggthmvctgrthtdrlcrfkwlcysseaeefiffhgnas
vmlpslgsrrfqpalldlstvedhntqyfnfvelpaaalrfmpkpvfvpdvalianrfnp
dnlmhvfhddllplfytlrqfpglarearlffmegwgegahfdlykllspkqpllraqlk
algrllcfshafvglskvttwyqygfvqpqgpkanilvsgneirqfahflmeklnvsqag
gplgeeyilvfsrtqnrlilneaelllalaqefqmktvtvsledhafadvvrlvsnasml
vsmhgaqlvtalflprgaavvelfpyavnpdhytpyktlatlpgmdlqyiawqntmpent
vthperpwdqggiahldraeqarilqsrevprhlccrnpewlfriyqdtkvdipsliqti
rrvvkghpgprkqkwtvslypgkvrearcqasvqgasearlsvswqipwnlkylkvrevk
yevwlqeqgentyvpymlalqnhtftenikpfttylvwircifnktllgpfadvlvcst

    Sequence, based on observed residues (ATOM records):
    >7e9kA (A:)
papalridypkalqilteggthmvctgrthtdrlcrfkwlcysseaeefiffhgnasvml
pslgsrrfqpalldlstvedhntqyfnfvelpaaalrfmpkpvfvpdvalianrfnpdnl
mhvfhddllplfytlrqfpglarearlffmegwgegahfdlykllspkqpllraqlkalg
rllcfshafvglskvttwyqygfvqpqgpkanilvsgneirqfahflmeklnvseeyilv
fsrtqnrlilneaelllalaqefqmktvtvsledhafadvvrlvsnasmlvsmhgaqlvt
alflprgaavvelfpyavnpdhytpyktlatlpgmdlqyiawqntmpentvthperpwdq
ggiahldraeqarilqsrevprhlccrnpewlfriyqdtkvdipsliqtirrvvkghpgp
rkqkwtvslypgkvrearcqasvasearlsvswqipwnlkylkvrevkyevwlqeqgent
yvpymlalqnhtftenikpfttylvwircifnktllgpfadvlvcst

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7e9kB (B:)
gappapalridypkalqilteggthmvctgrthtdrlcrfkwlcysseaeefiffhgnas
vmlpslgsrrfqpalldlstvedhntqyfnfvelpaaalrfmpkpvfvpdvalianrfnp
dnlmhvfhddllplfytlrqfpglarearlffmegwgegahfdlykllspkqpllraqlk
algrllcfshafvglskvttwyqygfvqpqgpkanilvsgneirqfahflmeklnvsqag
gplgeeyilvfsrtqnrlilneaelllalaqefqmktvtvsledhafadvvrlvsnasml
vsmhgaqlvtalflprgaavvelfpyavnpdhytpyktlatlpgmdlqyiawqntmpent
vthperpwdqggiahldraeqarilqsrevprhlccrnpewlfriyqdtkvdipsliqti
rrvvkghpgprkqkwtvslypgkvrearcqasvqgasearlsvswqipwnlkylkvrevk
yevwlqeqgentyvpymlalqnhtftenikpfttylvwircifnktllgpfadvlvcst

    Sequence, based on observed residues (ATOM records):
    >7e9kB (B:)
apalrypkalqilteggthmvctgrthtdrlcrfkwlcysseaeefiffhgnasvmlpsl
gsrrfqpalldlstvedhntqyfnfvelpaaalrfmpkpvfvpdvalianrfnpdnlmhv
fhddllplfytlrqfpglarearlffmegwgegahfdlykllspkqpllraqlkalgrll
cfshafvglskvttwyqygfvqpqgpkanilvsgneirqfahflmeklnvsqeeyilvfs
rtqnrlilneaelllalaqefqmktvtvsledhafadvvrlvsnasmlvsmhgaqlvtal
flprgaavvelfpyavnpdhytpyktlatlpgmdlqyiawqntmpentvthperpwdqgg
iahldraeqarilqsrevprhlccrnpewlfriyqdtkvdipsliqtirrvvkghpgpqk
wtvslypgkvrearcqassearlsvswqipwnlkylkvrevkyevwlqeqgentyvpyml
alqnhtftenikpfttylvwircifnktllgpfadvlvcst

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7e9kC (C:)
tirtrgaiiqtptlgpiqptr

    Sequence, based on observed residues (ATOM records):
    >7e9kC (C:)
rtrgaiiqtptlgpiqptr

  • Chain 'D':
    Sequence, based on SEQRES records:
    >7e9kD (D:)
gappapalridypkalqilteggthmvctgrthtdrlcrfkwlcysseaeefiffhgnas
vmlpslgsrrfqpalldlstvedhntqyfnfvelpaaalrfmpkpvfvpdvalianrfnp
dnlmhvfhddllplfytlrqfpglarearlffmegwgegahfdlykllspkqpllraqlk
algrllcfshafvglskvttwyqygfvqpqgpkanilvsgneirqfahflmeklnvsqag
gplgeeyilvfsrtqnrlilneaelllalaqefqmktvtvsledhafadvvrlvsnasml
vsmhgaqlvtalflprgaavvelfpyavnpdhytpyktlatlpgmdlqyiawqntmpent
vthperpwdqggiahldraeqarilqsrevprhlccrnpewlfriyqdtkvdipsliqti
rrvvkghpgprkqkwtvslypgkvrearcqasvqgasearlsvswqipwnlkylkvrevk
yevwlqeqgentyvpymlalqnhtftenikpfttylvwircifnktllgpfadvlvcst

    Sequence, based on observed residues (ATOM records):
    >7e9kD (D:)
papalridypkalqilteggthmvctgrthtdrlcrfkwlcysseaeefiffhgnasvml
pslgsrrfqpalldlstvedhntqyfnfvelpaaalrfmpkpvfvpdvalianrfnpdnl
mhvfhddllplfytlrqfpglarearlffmegwgegahfdlykllspkqpllraqlkalg
rllcfshafvglskvttwyqygfvqpqgpkanilvsgneirqfahflmeklnvseeyilv
fsrtqnrlilneaelllalaqefqmktvtvsledhafadvvrlvsnasmlvsmhgaqlvt
alflprgaavvelfpyavnpdhytpyktlatlpgmdlqyiawqntmpentvthperpwdq
ggiahldraeqarilqsrevprhlccrnpewlfriyqdtkvdipsliqtirrvvkghpgp
kqkwtvslypgkvrearcqasasearlsvswqipwnlkylkvrevkyevwlqeqgentyv
pymlalqnhtftenikpfttylvwircifnktllgpfadvlvcst

  • Chain 'E':
    Sequence, based on SEQRES records:
    >7e9kE (E:)
gappapalridypkalqilteggthmvctgrthtdrlcrfkwlcysseaeefiffhgnas
vmlpslgsrrfqpalldlstvedhntqyfnfvelpaaalrfmpkpvfvpdvalianrfnp
dnlmhvfhddllplfytlrqfpglarearlffmegwgegahfdlykllspkqpllraqlk
algrllcfshafvglskvttwyqygfvqpqgpkanilvsgneirqfahflmeklnvsqag
gplgeeyilvfsrtqnrlilneaelllalaqefqmktvtvsledhafadvvrlvsnasml
vsmhgaqlvtalflprgaavvelfpyavnpdhytpyktlatlpgmdlqyiawqntmpent
vthperpwdqggiahldraeqarilqsrevprhlccrnpewlfriyqdtkvdipsliqti
rrvvkghpgprkqkwtvslypgkvrearcqasvqgasearlsvswqipwnlkylkvrevk
yevwlqeqgentyvpymlalqnhtftenikpfttylvwircifnktllgpfadvlvcst

    Sequence, based on observed residues (ATOM records):
    >7e9kE (E:)
palridypkalqilteggthmvctgrthtdrlcrfkwlcysseaeefiffhgnasvmlps
lgsrrfqpalldlstvedhntqyfnfvelpaaalrfmpkpvfvpdvalianrfnpdnlmh
vfhddllplfytlrqfpglarearlffmegwgegahfdlykllspkqpllraqlkalgrl
lcfshafvglskvttwyqygfvqpqgpkanilvsgneirqfahflmeklnvseeyilvfs
rtqnrlilneaelllalaqefqmktvtvsledhafadvvrlvsnasmlvsmhgaqlvtal
flprgaavvelfpyavnpdhytpyktlatlpgmdlqyiawqntmpentvthperpwdqgg
iahldraeqarilqsrevprhlccrnpewlfriyqdtkvdipsliqtirrvvkghpgpkq
kwtvslypgkvrearcqasvqsearlsvswqipwnlkylkvrevkyevwlqeqgentyvp
ymlalqnhtftenikpfttylvwircifnktllgpfadvlvcst

  • Chain 'F':
    Sequence, based on SEQRES records:
    >7e9kF (F:)
tirtrgaiiqtptlgpiqptr

    Sequence, based on observed residues (ATOM records):
    >7e9kF (F:)
irtrgaiiqtptlgpiqptr