PDB entry 6nya

View 6nya on RCSB PDB site
Description: Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin
Class: ligase/transferase
Keywords: CONFORMATIONAL CHANGE, THIOESTER, ADENYLATION, THIOESTER TRANSFER, TRANSTHIOESTERIFICATION, ATP-BINDING, UBIQUITIN E2-BINDING, UBIQUITINATION, LIGASE, LIGASE-TRANSFERASE complex
Deposited on 2019-02-11, released 2019-08-07
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-01-01, with a file datestamp of 2019-12-27.
Experiment type: XRAY
Resolution: 2.07 Å
R-factor: N/A
AEROSPACI score: 0.3 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Ubiquitin-activating enzyme E1 1
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: UBA1, YKL210W
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Ubiquitin
    Species: TRITICUM AESTIVUM [TaxId:4565]
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A1D6RLC6 (9-84)
      • expression tag (7-8)
      • engineered mutation (14)
      • engineered mutation (19)
      • engineered mutation (35)
      • engineered mutation (37)
      • engineered mutation (41)
      • engineered mutation (56)
      • engineered mutation (71)
    Domains in SCOPe 2.08: d6nyab1, d6nyab2
  • Chain 'C':
    Compound: Ubiquitin-conjugating enzyme E2-34 kDa
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: CDC34, DNA6, UBC3, YDR054C, D4211, YD9609.08C
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6nyac_
  • Chain 'D':
    Compound: Ubiquitin-activating enzyme E1 1
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: UBA1, YKL210W
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Ubiquitin
    Species: TRITICUM AESTIVUM [TaxId:4565]
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A1D6RLC6 (9-84)
      • expression tag (8)
      • engineered mutation (14)
      • engineered mutation (19)
      • engineered mutation (35)
      • engineered mutation (37)
      • engineered mutation (41)
      • engineered mutation (56)
      • engineered mutation (71)
    Domains in SCOPe 2.08: d6nyae1, d6nyae2
  • Chain 'F':
    Compound: Ubiquitin-conjugating enzyme E2-34 kDa
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: CDC34, DNA6, UBC3, YDR054C, D4211, YD9609.08C
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6nyaf_
  • Heterogens: ATP, MG, SO4, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6nyaB (B:)
mhhhhhhgamqifvrtltgrtitlevessdtidnvrariqdregippdqqrlifagrqle
dgrtladyniqrestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6nyaB (B:)
gamqifvrtltgrtitlevessdtidnvrariqdregippdqqrlifagrqledgrtlad
yniqrestlhlvlrlrgg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6nyaC (C:)
gamasrkstasslllrqyreltdpkkaipsfhieleddsniftwnigvmvlnedsiyhgg
ffkaqmrfpedfpfsppqfrftpaiyhpnvyrdgrlcisilhqsgdpmtdepdaetwspv
qtvesvlisivslledpninspanvdaavdyrknpeqykqrvkmeverskqdipkgfimp
tsesayisqskldepes

    Sequence, based on observed residues (ATOM records): (download) 
    >6nyaC (C:)
srkstasslllrqyreltdpkkaipsfhieleddsniftwnigvmvlnedsiyhggffka
qmrfpedfpfsppqfrftpaiyhpnvyrdgrlcisilhqsaetwspvqtvesvlisivsl
ledpninspanvdaavdyrknpeqykqrvkmeverskqdipkgfimptse

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6nyaE (E:)
mhhhhhhgamqifvrtltgrtitlevessdtidnvrariqdregippdqqrlifagrqle
dgrtladyniqrestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6nyaE (E:)
amqifvrtltgrtitlevessdtidnvrariqdregippdqqrlifagrqledgrtlady
niqrestlhlvlrlrgg

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6nyaF (F:)
gamasrkstasslllrqyreltdpkkaipsfhieleddsniftwnigvmvlnedsiyhgg
ffkaqmrfpedfpfsppqfrftpaiyhpnvyrdgrlcisilhqsgdpmtdepdaetwspv
qtvesvlisivslledpninspanvdaavdyrknpeqykqrvkmeverskqdipkgfimp
tsesayisqskldepes

    Sequence, based on observed residues (ATOM records): (download) 
    >6nyaF (F:)
kstasslllrqyreltdpkkaipsfhieleddsniftwnigvmvlnedsiyhggffkaqm
rfpedfpfsppqfrftpaiyhpnvyrdgrlcisilhqsgdpetwspvqtvesvlisivsl
ledpninspanvdaavdyrknpeqykqrvkmeverskqdipkgfimp