PDB entry 5knl

View 5knl on RCSB PDB site
Description: Crystal structure of S. pombe ubiquitin E1 (Uba1) in complex with Ubc15 and ubiquitin
Class: ligase
Keywords: UBIQUITIN, E1, E2, UBA1, UBC15, CONFORMATIONAL CHANGE, THIOESTER, ADENYLATION, THIOESTER TRANSFER (TRANSTHIOESTERIFICATION), ATP-Binding, UBIQUITIN E2 BINDING, UBIQUITINATION, LIGASE
Deposited on 2016-06-28, released 2017-02-15
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-12-25, with a file datestamp of 2019-12-20.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Ubiquitin-activating enzyme E1 1
    Species: Schizosaccharomyces pombe (strain 972 / ATCC 24843) [TaxId:284812]
    Gene: ptr3, SPBC1604.21c, SPBC211.09
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Ubiquitin
    Species: Pseudozyma antarctica [TaxId:84753]
    Gene: PAN0_008c3613
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A081CFF0 (20-95)
      • engineered mutation (25)
      • engineered mutation (30)
      • engineered mutation (46)
      • engineered mutation (48)
      • engineered mutation (52)
      • engineered mutation (67)
      • engineered mutation (76)
      • engineered mutation (82)
    Domains in SCOPe 2.08: d5knlb_
  • Chain 'C':
    Compound: Ubiquitin-conjugating enzyme E2 15
    Species: Schizosaccharomyces pombe (strain 972 / ATCC 24843) [TaxId:284812]
    Gene: ubc15, SPBC1105.09
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9Y818 (0-166)
      • expression tag (167-170)
    Domains in SCOPe 2.08: d5knlc1, d5knlc2
  • Chain 'D':
    Compound: Ubiquitin-activating enzyme E1 1
    Species: Schizosaccharomyces pombe (strain 972 / ATCC 24843) [TaxId:284812]
    Gene: ptr3, SPBC1604.21c, SPBC211.09
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Ubiquitin
    Species: Pseudozyma antarctica [TaxId:84753]
    Gene: PAN0_008c3613
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A081CFF0 (20-95)
      • engineered mutation (25)
      • engineered mutation (30)
      • engineered mutation (46)
      • engineered mutation (48)
      • engineered mutation (52)
      • engineered mutation (67)
      • engineered mutation (76)
      • engineered mutation (82)
    Domains in SCOPe 2.08: d5knle_
  • Chain 'F':
    Compound: Ubiquitin-conjugating enzyme E2 15
    Species: Schizosaccharomyces pombe (strain 972 / ATCC 24843) [TaxId:284812]
    Gene: ubc15, SPBC1105.09
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9Y818 (0-166)
      • expression tag (167-170)
    Domains in SCOPe 2.08: d5knlf1, d5knlf2
  • Heterogens: SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5knlB (B:)
mgsshhhhhhssglvprgshmqifvrtltgrtitlevessdtidnvrariqdregippdq
qrlifagrqledgrtladyniqrestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >5knlB (B:)
mqifvrtltgrtitlevessdtidnvrariqdregippdqqrlifagrqledgrtladyn
iqrestlhlvlrlrgg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5knlC (C:)
mpssaseqllrkqlkeiqknppqgfsvglvddksifewevmiigpedtlyeggffhatls
fpqdyplmppkmkftteiwhpnvhpngevcisilhppgddkygyedagerwlpvhspeti
lisvismlsspndespanidaakefrenpqefkkrvrrlvrrsiemilehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >5knlC (C:)
mpssaseqllrkqlkeiqknppqgfsvglvddksifewevmiigpedtlyeggffhatls
fpqdyplmppkmkftteiwhpnvhpngevcisilhppgddkygyedagerwlpvhspeti
lisvismlsspndespanidaakefrenpqefkkrvrrlvrrsiemilehh

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5knlE (E:)
mgsshhhhhhssglvprgshmqifvrtltgrtitlevessdtidnvrariqdregippdq
qrlifagrqledgrtladyniqrestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >5knlE (E:)
mqifvrtltgrtitlevessdtidnvrariqdregippdqqrlifagrqledgrtladyn
iqrestlhlvlrlrgg

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5knlF (F:)
mpssaseqllrkqlkeiqknppqgfsvglvddksifewevmiigpedtlyeggffhatls
fpqdyplmppkmkftteiwhpnvhpngevcisilhppgddkygyedagerwlpvhspeti
lisvismlsspndespanidaakefrenpqefkkrvrrlvrrsiemilehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >5knlF (F:)
mpssaseqllrkqlkeiqknppqgfsvglvddksifewevmiigpedtlyeggffhatls
fpqdyplmppkmkftteiwhpnvhpngevcisilhppgderwlpvhspetilisvismls
spndespanidaakefrenpqefkkrvrrlvrrsiemilehh