PDB entry 6w9d

View 6w9d on RCSB PDB site
Description: RNF12 RING domain in complex with a Ube2d2~Ub conjugate
Class: ligase
Keywords: RING E3 ligase, Ubiquitin, Ubiquitin conjugating enzyme, X-chromosome inactivation, RING, LIGASE
Deposited on 2020-03-22, released 2020-05-20
The last revision prior to the SCOPe 2.07 freeze date was dated 2020-05-20, with a file datestamp of 2020-05-15.
Experiment type: XRAY
Resolution: 3.19 Å
R-factor: N/A
AEROSPACI score: 0.12 (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 (Start-146)
      • engineered mutation (20-21)
      • engineered mutation (84)
      • engineered mutation (106)
      • engineered mutation (110)
      • expression tag (147-148)
    Domains in SCOPe 2.07: d6w9da1, d6w9da2
  • Chain 'B':
    Compound: E3 ubiquitin-protein ligase RLIM
    Species: Homo sapiens [TaxId:9606]
    Gene: RLIM, RNF12
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6w9dc_
  • 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 (Start-146)
      • engineered mutation (20-21)
      • engineered mutation (84)
      • engineered mutation (106)
      • engineered mutation (110)
      • expression tag (147-148)
    Domains in SCOPe 2.07: d6w9dd1, d6w9dd2
  • Chain 'E':
    Compound: E3 ubiquitin-protein ligase RLIM
    Species: Homo sapiens [TaxId:9606]
    Gene: RLIM, RNF12
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6w9df_
  • 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 (0-146)
      • engineered mutation (20-21)
      • engineered mutation (84)
      • engineered mutation (106)
      • engineered mutation (110)
      • expression tag (147)
    Domains in SCOPe 2.07: d6w9dg1, d6w9dg2
  • Chain 'H':
    Compound: E3 ubiquitin-protein ligase RLIM
    Species: Homo sapiens [TaxId:9606]
    Gene: RLIM, RNF12
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6w9di_
  • Heterogens: ZN, IOD

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6w9dA (A:)
malkrihkelndlardppaqsragpvgddmfhwqatimgpndspyqggvffltihfptdy
pfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddplv
peiariyktdrekynriarewtqkyamlehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6w9dA (A:)
alkrihkelndlardppaqsragpvgddmfhwqatimgpndspyqggvffltihfptdyp
fkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddplvp
eiariyktdrekynriarewtqkyamle

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6w9dC (C:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6w9dC (C:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlr

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6w9dD (D:)
malkrihkelndlardppaqsragpvgddmfhwqatimgpndspyqggvffltihfptdy
pfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddplv
peiariyktdrekynriarewtqkyamlehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6w9dD (D:)
alkrihkelndlardppaqsragpvgddmfhwqatimgpndspyqggvffltihfptdyp
fkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddplvp
eiariyktdrekynriarewtqkyamle

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6w9dF (F:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6w9dF (F:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlv

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6w9dG (G:)
malkrihkelndlardppaqsragpvgddmfhwqatimgpndspyqggvffltihfptdy
pfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddplv
peiariyktdrekynriarewtqkyamlehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6w9dG (G:)
malkrihkelndlardppaqsragpvgddmfhwqatimgpndspyqggvffltihfptdy
pfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsissllsdpnpddplv
peiariyktdrekynriarewtqkyaml

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >6w9dI (I:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6w9dI (I:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlr