PDB entry 5ydk

View 5ydk on RCSB PDB site
Description: Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form
Class: signaling protein
Keywords: ubiquitin, SIGNALING PROTEIN
Deposited on 2017-09-13, released 2018-03-07
The last revision prior to the SCOPe 2.08 freeze date was dated 2018-03-21, with a file datestamp of 2018-03-16.
Experiment type: XRAY
Resolution: 2.51 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: E3 ubiquitin-protein ligase RNF168
    Species: Homo sapiens [TaxId:9606]
    Gene: RNF168
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8IYW5 (5-End)
      • expression tag (3-4)
  • Chain 'B':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62979 (0-75)
      • engineered mutation (62)
    Domains in SCOPe 2.08: d5ydkb_
  • Chain 'C':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ydkc_
  • Chain 'D':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ydkd_
  • Chain 'E':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62979 (0-75)
      • engineered mutation (62)
    Domains in SCOPe 2.08: d5ydke_
  • Chain 'F':
    Compound: E3 ubiquitin-protein ligase RNF168
    Species: Homo sapiens [TaxId:9606]
    Gene: RNF168
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8IYW5 (5-End)
      • expression tag (2-4)
  • Chain 'G':
    Compound: E3 ubiquitin-protein ligase RNF168
    Species: Homo sapiens [TaxId:9606]
    Gene: RNF168
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8IYW5 (5-End)
      • expression tag (4)
  • Chain 'H':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62979 (0-75)
      • engineered mutation (62)
    Domains in SCOPe 2.08: d5ydkh_
  • Chain 'I':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ydki_
  • Chain 'J':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ydkj_
  • Chain 'K':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: Rps27a, Uba80, Ubcep1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62979 (0-75)
      • engineered mutation (62)
    Domains in SCOPe 2.08: d5ydkk_
  • Chain 'L':
    Compound: E3 ubiquitin-protein ligase RNF168
    Species: Homo sapiens [TaxId:9606]
    Gene: RNF168
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8IYW5 (5-End)
      • expression tag (2-4)
  • Heterogens: GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5ydkB (B:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqrestlhlvlrlrgg
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5ydkC (C:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrggd
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ydkC (C:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5ydkD (D:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrggd
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ydkD (D:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrg
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5ydkE (E:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqrestlhlvlrlrgg
    

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5ydkH (H:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqrestlhlvlrlrgg
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >5ydkI (I:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrggd
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ydkI (I:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrl
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >5ydkJ (J:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrggd
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ydkJ (J:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrl
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5ydkK (K:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqrestlhlvlrlrgg
    

  • Chain 'L':
    No sequence available.