PDB entry 5d0k

View 5d0k on RCSB PDB site
Description: Structure of UbE2D2:RNF165:Ub complex
Class: ligase
Keywords: complex, ubiquitin, LIGASE
Deposited on 2015-08-03, released 2015-12-09
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-01-20, with a file datestamp of 2016-01-15.
Experiment type: XRAY
Resolution: 2.65 Å
R-factor: N/A
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: ubiquitin-conjugating enzyme e2 d2
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62837 (5-151)
      • expression tag (4)
      • engineered mutation (25)
      • engineered mutation (89)
      • engineered mutation (111)
      • engineered mutation (115)
    Domains in SCOPe 2.07: d5d0ka1, d5d0ka2
  • Chain 'B':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d0kb_
  • Chain 'C':
    Compound: RING finger protein 165
    Species: Homo sapiens [TaxId:9606]
    Gene: RNF165
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: ubiquitin-conjugating enzyme e2 d2
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62837 (5-151)
      • expression tag (4)
      • engineered mutation (25)
      • engineered mutation (89)
      • engineered mutation (111)
      • engineered mutation (115)
    Domains in SCOPe 2.07: d5d0kd1, d5d0kd2
  • Chain 'E':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d0ke_
  • Chain 'F':
    Compound: RING finger protein 165
    Species: Homo sapiens [TaxId:9606]
    Gene: RNF165
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: ubiquitin-conjugating enzyme e2 d2
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62837 (5-151)
      • expression tag (4)
      • engineered mutation (25)
      • engineered mutation (89)
      • engineered mutation (111)
      • engineered mutation (115)
    Domains in SCOPe 2.07: d5d0kg1, d5d0kg2
  • Chain 'H':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d0kh_
  • Chain 'I':
    Compound: RING finger protein 165
    Species: Homo sapiens [TaxId:9606]
    Gene: RNF165
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: ubiquitin-conjugating enzyme e2 d2
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62837 (5-151)
      • expression tag (4)
      • engineered mutation (25)
      • engineered mutation (89)
      • engineered mutation (111)
      • engineered mutation (115)
    Domains in SCOPe 2.07: d5d0kj1, d5d0kj2
  • Chain 'K':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d0kk_
  • Chain 'L':
    Compound: RING finger protein 165
    Species: Homo sapiens [TaxId:9606]
    Gene: RNF165
    Database cross-references and differences (RAF-indexed):
  • Heterogens: ZN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5d0kA (A:)
    gplgsmalkrihkelndlardppaqssagpvgddmfhwqatimgpndspyqggvffltih
    fptdypfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnp
    ddplvpeiariyktdrekynriarewtqkyam
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d0kA (A:)
    smalkrihkelndlardppaqssagpvgddmfhwqatimgpndspyqggvffltihfptd
    ypfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddpl
    vpeiariyktdrekynriarewtqkyam
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5d0kB (B:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrgg
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5d0kD (D:)
    gplgsmalkrihkelndlardppaqssagpvgddmfhwqatimgpndspyqggvffltih
    fptdypfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnp
    ddplvpeiariyktdrekynriarewtqkyam
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d0kD (D:)
    smalkrihkelndlardppaqssagpvgddmfhwqatimgpndspyqggvffltihfptd
    ypfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddpl
    vpeiariyktdrekynriarewtqkyam
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5d0kE (E:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrgg
    

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5d0kG (G:)
    gplgsmalkrihkelndlardppaqssagpvgddmfhwqatimgpndspyqggvffltih
    fptdypfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnp
    ddplvpeiariyktdrekynriarewtqkyam
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d0kG (G:)
    smalkrihkelndlardppaqssagpvgddmfhwqatimgpndspyqggvffltihfptd
    ypfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddpl
    vpeiariyktdrekynriarewtqkyam
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5d0kH (H:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrgg
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >5d0kJ (J:)
    gplgsmalkrihkelndlardppaqssagpvgddmfhwqatimgpndspyqggvffltih
    fptdypfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnp
    ddplvpeiariyktdrekynriarewtqkyam
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d0kJ (J:)
    smalkrihkelndlardppaqssagpvgddmfhwqatimgpndspyqggvffltihfptd
    ypfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddpl
    vpeiariyktdrekynriarewtqkyam
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5d0kK (K:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrgg
    

  • Chain 'L':
    No sequence available.