PDB entry 3nxd

View 3nxd on RCSB PDB site
Description: JC polyomavirus VP1 in complex with LSTc
Class: viral protein
Keywords: beta-sandwich with jelly roll topology, major capsid protein, VIRAL PROTEIN
Deposited on 2010-07-13, released 2010-11-17
The last revision prior to the SCOPe 2.07 freeze date was dated 2010-11-17, with a file datestamp of 2010-11-12.
Experiment type: XRAY
Resolution: 2 Å
R-factor: 0.18
AEROSPACI score: 0.45 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Gene: VP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3nxda_
  • Chain 'B':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Gene: VP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3nxdb_
  • Chain 'C':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Gene: VP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3nxdc_
  • Chain 'D':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Gene: VP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3nxdd_
  • Chain 'E':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Gene: VP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3nxde_
  • Heterogens: GOL, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3nxdA (A:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgsqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nxdA (A:)
    vevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysva
    riplpnlnilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvggea
    lelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrnent
    ryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgsqq
    wrglsryfkvqlrkrrvkn
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3nxdB (B:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgsqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nxdB (B:)
    evlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysvar
    iplpnlnilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvggeal
    elqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrnentr
    yfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgsqqw
    rglsryfkvqlrkrrvkn
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3nxdC (C:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgsqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nxdC (C:)
    evlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysvar
    iplpnlnedlilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvgg
    ealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrne
    ntryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgs
    qqwrglsryfkvqlrkrrvkn
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3nxdD (D:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgsqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nxdD (D:)
    evlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysvar
    iplpnlnedlilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvgg
    ealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrne
    ntryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgs
    qqwrglsryfkvqlrkrrvkn
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3nxdE (E:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgsqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nxdE (E:)
    evlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysvar
    iplpnlnilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvggeal
    elqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrnentr
    yfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgsqqw
    rglsryfkvqlrkrrvkn