PDB entry 5ydr

View 5ydr on RCSB PDB site
Description: Structure of DNMT1 RFTS domain in complex with ubiquitin
Class: protein binding/transferase
Keywords: DNA methylation, PROTEIN BINDING, PROTEIN BINDING-TRANSFERASE complex
Deposited on 2017-09-14, released 2018-02-21
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-02-21, with a file datestamp of 2018-02-16.
Experiment type: XRAY
Resolution: 2 Å
R-factor: N/A
AEROSPACI score: 0.33 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed):
    • Uniprot J3QS39 (2-74)
      • expression tag (0-1)
    Domains in SCOPe 2.07: d5ydra1, d5ydra2
  • Chain 'B':
    Compound: DNA (cytosine-5)-methyltransferase 1
    Species: Homo sapiens [TaxId:9606]
    Gene: DNMT1, AIM, CXXC9, DNMT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P26358 (1-249)
      • expression tag (0)
  • Chain 'D':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed):
    • Uniprot J3QS39 (2-End)
      • expression tag (1)
    Domains in SCOPe 2.07: d5ydrd1, d5ydrd2
  • Heterogens: PO4, ZN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5ydrA (A:)
    ahmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsd
    yniqkestlhlvlrl
    

  • Chain 'B':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5ydrD (D:)
    ahmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsd
    yniqkestlhlvlrl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ydrD (D:)
    hmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
    niqkestlhlvlr