PDB entry 5y3d

View 5y3d on RCSB PDB site
Description: Structural insight into the interaction between RNA polymerase and VPg for norovirus replication
Class: viral protein
Keywords: norovirus, RNA-dependent RNA polymerase, VPg, interaction, viral replication, VIRAL PROTEIN
Deposited on 2017-07-28, released 2018-07-18
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-07-18, with a file datestamp of 2018-07-13.
Experiment type: XRAY
Resolution: 3.14 Å
R-factor: N/A
AEROSPACI score: 0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: RNA-dependent RNA polymerase
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5y3da_
  • Chain 'B':
    Compound: RNA-dependent RNA polymerase
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5y3db_
  • Chain 'C':
    Compound: RNA-dependent RNA polymerase
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5y3dc_
  • Chain 'D':
    Compound: RNA-dependent RNA polymerase
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5y3dd_
  • Chain 'E':
    Compound: RNA-dependent RNA polymerase
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5y3de_
  • Chain 'F':
    Compound: RNA-dependent RNA polymerase
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5y3df_
  • Chain 'G':
    Compound: viral protein genome-linked (VPg)
    Species: Murine norovirus [TaxId:357231]
    Database cross-references and differences (RAF-indexed):
    • PDB 5Y3D (0-34)
  • Chain 'H':
    Compound: viral protein genome-linked (VPg)
    Species: Murine norovirus [TaxId:357231]
    Database cross-references and differences (RAF-indexed):
    • PDB 5Y3D (0-34)
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5y3dA (A:)
    mlprpsgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslq
    qvmrdqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssg
    ypyhkqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkik
    krllwgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmd
    adytrwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglps
    gcpcttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytm
    alrrygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkg
    pnhqnpfetlpghaqrpsqlmallgeaamhgekyyrtvasrvskeaaqsgiemvvprhrs
    vlrwvrfgtmdaetpqersavfvnedaaalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5y3dA (A:)
    psgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslqqvmr
    dqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssgypyh
    kqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkikkrll
    wgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmdadyt
    rwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglpsgcpc
    ttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytmalrr
    ygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkgpnhq
    npfetlpaqrpsqlmallgeaamhgekyyrtvasrvskeaaqsgvvprhrsvlrwvrfg
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5y3dB (B:)
    mlprpsgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslq
    qvmrdqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssg
    ypyhkqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkik
    krllwgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmd
    adytrwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglps
    gcpcttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytm
    alrrygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkg
    pnhqnpfetlpghaqrpsqlmallgeaamhgekyyrtvasrvskeaaqsgiemvvprhrs
    vlrwvrfgtmdaetpqersavfvnedaaalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5y3dB (B:)
    psgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslqqvmr
    dqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssgypyh
    kqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkikkrll
    wgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmdadyt
    rwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglpsgcpc
    ttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytmalrr
    ygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkgpnhq
    npfetlpgsqlmallgeaamhgekyyrtvasrvskeaaqsgiemvvprhrsvlrwvrfg
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5y3dC (C:)
    mlprpsgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslq
    qvmrdqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssg
    ypyhkqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkik
    krllwgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmd
    adytrwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglps
    gcpcttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytm
    alrrygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkg
    pnhqnpfetlpghaqrpsqlmallgeaamhgekyyrtvasrvskeaaqsgiemvvprhrs
    vlrwvrfgtmdaetpqersavfvnedaaalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5y3dC (C:)
    psgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslqqvmr
    dqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssgypyh
    kqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkikkrll
    wgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmdadyt
    rwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglpsgcpc
    ttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytmalrr
    ygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkgpnhq
    npfetlpghrpsqlmallgeaamhgekyyrtvasrvskeaaqsgmvvprhrsvlrwvrfg
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5y3dD (D:)
    mlprpsgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslq
    qvmrdqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssg
    ypyhkqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkik
    krllwgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmd
    adytrwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglps
    gcpcttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytm
    alrrygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkg
    pnhqnpfetlpghaqrpsqlmallgeaamhgekyyrtvasrvskeaaqsgiemvvprhrs
    vlrwvrfgtmdaetpqersavfvnedaaalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5y3dD (D:)
    psgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslqqvmr
    dqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssgypyh
    kqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkikkrll
    wgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmdadyt
    rwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglpsgcpc
    ttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytmalrr
    ygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkgpnhq
    npfetlpghrpsqlmallgeaamhgekyyrtvasrvskeaaqsgvvprhrsvlrwvrfg
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5y3dE (E:)
    mlprpsgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslq
    qvmrdqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssg
    ypyhkqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkik
    krllwgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmd
    adytrwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglps
    gcpcttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytm
    alrrygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkg
    pnhqnpfetlpghaqrpsqlmallgeaamhgekyyrtvasrvskeaaqsgiemvvprhrs
    vlrwvrfgtmdaetpqersavfvnedaaalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5y3dE (E:)
    psgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslqqvmr
    dqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssgypyh
    kqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkikkrll
    wgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmdadyt
    rwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglpsgcpc
    ttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytmalrr
    ygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkgpnhq
    npfetlpghrpsqlmallgeaamhgekyyrtvasrvskeaaqsgiemvvprhrsvlrwvr
    fgt
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5y3dF (F:)
    mlprpsgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslq
    qvmrdqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssg
    ypyhkqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkik
    krllwgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmd
    adytrwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglps
    gcpcttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytm
    alrrygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkg
    pnhqnpfetlpghaqrpsqlmallgeaamhgekyyrtvasrvskeaaqsgiemvvprhrs
    vlrwvrfgtmdaetpqersavfvnedaaalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5y3dF (F:)
    psgtyaglpiadygdapplstktmfwrtspeklppgawepaylgskdervdgpslqqvmr
    dqlkpyseprgllppqeildavcdaienrlentlepqkpwtfkkacesldkntssgypyh
    kqkskdwtgsafigdlgdqathannmyemgksmrpiytaalkdelvkpdkiygkikkrll
    wgsdlgtmiraarafgpfcdalketcifnpirvgmsmnedgpfifarhanfryhmdadyt
    rwdstqqrailkragdimvrlspepdlarvvmddllapslldvgdykivveeglpsgcpc
    ttqlnslahwiltlcamvevtrvdpdivmqesefsfygddevvstnleldmvkytmalrr
    ygllptradkeegplerrqtlqgisflrraivgdqfgwygrldrasidrqllwtkgpnhq
    npfetlpghrpsqlmallgeaamhgekyyrtvasrvskeaaqsgmvvprhrsvlrwvrfg
    t
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.