PDB entry 3dqv

View 3dqv on RCSB PDB site
Description: Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation
Class: ligase
Keywords: ubiquitin, nedd8, scf, cullin-ring ligase, cullin, Nucleus, Ubl conjugation pathway, Host-virus interaction, Receptor, Ubl conjugation, Acetylation, Cytoplasm, DNA damage, DNA repair, Metal-binding, Zinc, Zinc-finger, SIGNALING PROTEIN
Deposited on 2008-07-09, released 2008-09-30
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-02-03.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.249
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (5-80)
      • insertion (3-4)
      • conflict (66)
    Domains in SCOPe 2.06: d3dqva2, d3dqva3
  • Chain 'B':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (5-80)
      • insertion (4)
      • conflict (66)
    Domains in SCOPe 2.06: d3dqvb1, d3dqvb2
  • Chain 'C':
    Compound: Cullin-5
    Species: Homo sapiens [TaxId:9606]
    Gene: CUL5, VACM1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q93034 (2-381)
      • conflict (8)
      • conflict (40-41)
  • Chain 'D':
    Compound: Cullin-5
    Species: Homo sapiens [TaxId:9606]
    Gene: CUL5, VACM1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q93034 (2-381)
      • conflict (8)
      • conflict (40-41)
  • Chain 'R':
    Compound: Rbx1
    Species: Homo sapiens [TaxId:9606]
    Gene: RBX1, RNF75, ROC1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dqvr_
  • Chain 'Y':
    Compound: Rbx1
    Species: Homo sapiens [TaxId:9606]
    Gene: RBX1, RNF75, ROC1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dqvy_
  • Heterogens: ZN

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3dqvA (A:)
    gsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndekt
    aadykimggsvlhlvlalrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dqvA (A:)
    gsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaad
    ykimggsvlhlvlalrgg
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3dqvB (B:)
    gsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndekt
    aadykimggsvlhlvlalrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dqvB (B:)
    smlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaady
    kimggsvlhlvlalrgg
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >3dqvR (R:)
    gsmdvdtpsgtnsgagkkrfevkkwnavalwawdivvdncaicrnhimdlciecqanqas
    atseectvawgvcnhafhfhcisrwlktrqvcpldnrewefqkygh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dqvR (R:)
    krfevkkwnavalwawdivvdncaicrnhimdlciecqanqasatseectvawgvcnhaf
    hfhcisrwlktrqvcpldnrewefqk
    

  • Chain 'Y':
    Sequence, based on SEQRES records: (download)
    >3dqvY (Y:)
    gsmdvdtpsgtnsgagkkrfevkkwnavalwawdivvdncaicrnhimdlciecqanqas
    atseectvawgvcnhafhfhcisrwlktrqvcpldnrewefqkygh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dqvY (Y:)
    kkrfevkkwnavalwawdivvdncaicrnhimciecqanqasatseectvawgvcnhafh
    fhcisrwlktrqvcpldnrewefqk