PDB entry 6sqr

View 6sqr on RCSB PDB site
Description: Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub
Class: ligase
Keywords: MDM2, MDMX, p53, E3, E2, ubiquitin, ubiquitin ligase, phosphorylation, LIGASE
Deposited on 2019-09-04, released 2020-05-06
The last revision prior to the SCOPe 2.07 freeze date was dated 2020-05-06, with a file datestamp of 2020-05-01.
Experiment type: XRAY
Resolution: 2.18 Å
R-factor: N/A
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: E3 ubiquitin-protein ligase Mdm2
    Species: Felis catus [TaxId:9685]
    Gene: MDM2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q7YRZ8 (0-68)
      • engineered mutation (6)
      • engineered mutation (20)
  • Chain 'B':
    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 (0-145)
      • engineered mutation (20)
      • engineered mutation (83)
    Domains in SCOPe 2.07: d6sqrb_
  • Chain 'C':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: RPS27A
    Database cross-references and differences (RAF-indexed):
    • Uniprot J3QTR3 (1-76)
      • expression tag (0)
    Domains in SCOPe 2.07: d6sqrc1, d6sqrc2
  • Chain 'D':
    Compound: E3 ubiquitin-protein ligase Mdm2
    Species: Felis catus [TaxId:9685]
    Gene: MDM2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q7YRZ8 (0-63)
      • engineered mutation (1)
      • engineered mutation (15)
  • 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 (0-145)
      • engineered mutation (20)
      • engineered mutation (83)
    Domains in SCOPe 2.07: d6sqre_
  • Chain 'F':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: RPS27A
    Database cross-references and differences (RAF-indexed):
    • Uniprot J3QTR3 (1-76)
      • expression tag (0)
    Domains in SCOPe 2.07: d6sqrf1, d6sqrf2
  • Chain 'G':
    Compound: E3 ubiquitin-protein ligase Mdm2
    Species: Felis catus [TaxId:9685]
    Gene: MDM2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q7YRZ8 (0-62)
      • engineered mutation (0)
      • engineered mutation (14)
  • Chain 'H':
    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 (0-145)
      • engineered mutation (20)
      • engineered mutation (83)
    Domains in SCOPe 2.07: d6sqrh_
  • Chain 'I':
    Compound: Polyubiquitin-C
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6sqri_
  • Chain 'J':
    Compound: E3 ubiquitin-protein ligase Mdm2
    Species: Felis catus [TaxId:9685]
    Gene: MDM2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q7YRZ8 (0-63)
      • engineered mutation (1)
      • engineered mutation (15)
  • Chain 'K':
    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 (0-145)
      • engineered mutation (20)
      • engineered mutation (83)
    Domains in SCOPe 2.07: d6sqrk_
  • Chain 'L':
    Compound: Ubiquitin-40S ribosomal protein S27a
    Species: Homo sapiens [TaxId:9606]
    Gene: RPS27A
    Database cross-references and differences (RAF-indexed):
    • Uniprot J3QTR3 (1-76)
      • expression tag (0)
    Domains in SCOPe 2.07: d6sqrl1, d6sqrl2
  • Heterogens: EDO, ZN, NO3, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6sqrB (B:)
alkrihkelndlardppaqcragpvgddmfhwqatimgpndspyqggvffltihfptdyp
fkppkvafttriyhpninsngsikldilrsqwspaltiskvllsicsllcdpnpddplvp
eiariyktdrekynriarewtqkyam

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6sqrC (C:)
smqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlrgg

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6sqrE (E:)
alkrihkelndlardppaqcragpvgddmfhwqatimgpndspyqggvffltihfptdyp
fkppkvafttriyhpninsngsikldilrsqwspaltiskvllsicsllcdpnpddplvp
eiariyktdrekynriarewtqkyam

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6sqrF (F:)
smqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlrgg

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6sqrH (H:)
alkrihkelndlardppaqcragpvgddmfhwqatimgpndspyqggvffltihfptdyp
fkppkvafttriyhpninsngsikldilrsqwspaltiskvllsicsllcdpnpddplvp
eiariyktdrekynriarewtqkyam

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6sqrI (I:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgg

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6sqrK (K:)
alkrihkelndlardppaqcragpvgddmfhwqatimgpndspyqggvffltihfptdyp
fkppkvafttriyhpninsngsikldilrsqwspaltiskvllsicsllcdpnpddplvp
eiariyktdrekynriarewtqkyam

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6sqrL (L:)
smqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlrgg