PDB entry 4jcd

View 4jcd on RCSB PDB site
Description: S268Y Variant of JC Polyomavirus Major Capsid Protein VP1
Class: viral protein
Keywords: beta-sandwich, jelly roll topology, viral protein, major capsid protein, PML-associated VP1 mutation
Deposited on 2013-02-21, released 2013-08-14
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-11-15, with a file datestamp of 2017-11-10.
Experiment type: XRAY
Resolution: 2 Å
R-factor: N/A
AEROSPACI score: 0.31 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03089
      • engineered mutation (250)
    Domains in SCOPe 2.07: d4jcda_
  • Chain 'B':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03089
      • engineered mutation (250)
    Domains in SCOPe 2.07: d4jcdb_
  • Chain 'C':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03089
      • engineered mutation (250)
    Domains in SCOPe 2.07: d4jcdc_
  • Chain 'D':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03089
      • engineered mutation (250)
    Domains in SCOPe 2.07: d4jcdd_
  • Chain 'E':
    Compound: Major capsid protein VP1
    Species: JC polyomavirus [TaxId:10632]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03089
      • engineered mutation (250)
    Domains in SCOPe 2.07: d4jcde_
  • Heterogens: GOL, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4jcdA (A:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgyqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4jcdA (A:)
    vevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysva
    riplpnlilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvggeal
    elqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrnentr
    yfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgyqqw
    rglsryfkvqlrkrrvk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4jcdB (B:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgyqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4jcdB (B:)
    vevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysva
    riplpnlnilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvggea
    lelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrnent
    ryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgyqq
    wrglsryfkvqlrkrrvk
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4jcdC (C:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgyqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4jcdC (C:)
    evlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysvar
    iplpnlilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvggeale
    lqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrnentry
    fgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgyqqwr
    glsryfkvqlrkrrvk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4jcdD (D:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgyqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4jcdD (D:)
    vevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysva
    riplpnlilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvggeal
    elqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrnentr
    yfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgyqqw
    rglsryfkvqlrkrrvk
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4jcdE (E:)
    gshmggvevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdml
    pcysvariplpnlnedltcgnilmweavtlktevigvtslmnvhsngqathdngagkpvq
    gtsfhffsvggealelqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypv
    ecwvpdptrnentryfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavd
    vcgmftnrsgyqqwrglsryfkvqlrkrrvkn
    

    Sequence, based on observed residues (ATOM records): (download)
    >4jcdE (E:)
    vevlevktgvdsitevecfltpemgdpdehlrgfsksisisdtfesdspnrdmlpcysva
    riplpnlilmweavtlktevigvtslmnvhsngqathdngagkpvqgtsfhffsvggeal
    elqgvlfnyrtkypdgtifpknatvqsqvmntehkayldknkaypvecwvpdptrnentr
    yfgtltggenvppvlhitntattvlldefgvgplckgdnlylsavdvcgmftnrsgyqqw
    rglsryfkvqlrkrrvk