PDB entry 5mnj

View 5mnj on RCSB PDB site
Description: Structure of MDM2-MDMX-UbcH5B-ubiquitin complex
Class: ligase
Keywords: Ubiquitin ligase, ligase
Deposited on 2016-12-13, released 2017-05-31
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-10-16, with a file datestamp of 2019-10-11.
Experiment type: XRAY
Resolution: 2.16 Å
R-factor: N/A
AEROSPACI score: 0.27 (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 (21)
      • engineered mutation (84)
    Domains in SCOPe 2.08: d5mnja_
  • Chain 'B':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5mnjb_
  • Chain 'C':
    Compound: E3 ubiquitin-protein ligase Mdm2
    Species: Homo sapiens [TaxId:9606]
    Gene: MDM2
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Protein Mdm4
    Species: Homo sapiens [TaxId:9606]
    Gene: mdm4, mdmx
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    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 (21)
      • engineered mutation (84)
    Domains in SCOPe 2.08: d5mnje_
  • Chain 'F':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5mnjf_
  • Chain 'G':
    Compound: E3 ubiquitin-protein ligase Mdm2
    Species: Homo sapiens [TaxId:9606]
    Gene: MDM2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q00987 (22-85)
      • expression tag (21)
  • Chain 'H':
    Compound: Protein Mdm4
    Species: Homo sapiens [TaxId:9606]
    Gene: mdm4, mdmx
    Database cross-references and differences (RAF-indexed):
  • Heterogens: ZN, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5mnjA (A:)
malkrihkelndlardppaqcragpvgddmfhwqatimgpndspyqggvffltihfptdy
pfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsicsllcdpnpddplv
peiariyktdrekynriarewtqkyam

    Sequence, based on observed residues (ATOM records): (download) 
    >5mnjA (A:)
alkrihkelndlardppaqcragpvgddmfhwqatimgpndspyqggvffltihfptdyp
fkppkvafttriyhpninsngsikldilrsqwspaltiskvllsicsllcdpnpddplvp
eiariyktdrekynriarewtqkyam

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5mnjB (B:)
gsggsmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrt
lsdyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >5mnjB (B:)
qifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyni
qkestlhlvlrlrgg

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5mnjE (E:)
malkrihkelndlardppaqcragpvgddmfhwqatimgpndspyqggvffltihfptdy
pfkppkvafttriyhpninsngsikldilrsqwspaltiskvllsicsllcdpnpddplv
peiariyktdrekynriarewtqkyam

    Sequence, based on observed residues (ATOM records): (download) 
    >5mnjE (E:)
alkrihkelndlardppaqcragpvgddmfhwqatimgpndspyqggvffltihfptdyp
fkppkvafttriyhpninsngsikldilrsqwspaltiskvllsicsllcdpnpddplvp
eiariyktdrekynriarewtqkyam

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5mnjF (F:)
gsggsmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrt
lsdyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >5mnjF (F:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgg

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.