PDB entry 4pot

View 4pot on RCSB PDB site
Description: Structure of Human Polyomavirus 9 VP1 pentamer in complex with N-glycolylneuraminic acid containing 3'-sialyllactosamine
Class: viral protein
Keywords: jelly roll fold, capsid formation, receptor interaction, carbohydrate, sialyloligosaccharide, viral coat protein, VIRAL PROTEIN
Deposited on 2014-02-26, released 2014-04-09
The last revision prior to the SCOPe 2.07 freeze date was dated 2014-11-26, with a file datestamp of 2014-11-21.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: 0.186
AEROSPACI score: 0.35 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4pota_
  • Chain 'B':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4potb_
  • Chain 'C':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4potc_
  • Chain 'D':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4potd_
  • Chain 'E':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4pote_
  • Chain 'F':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4potf_
  • Chain 'G':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4potg_
  • Chain 'H':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4poth_
  • Chain 'I':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4poti_
  • Chain 'J':
    Compound: vp1
    Species: Human Polyomavirus 9 [TaxId:943908]
    Gene: gp3, vp1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4potj_
  • Heterogens: CA, EDO, IPA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4potA (A:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potA (A:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlnemtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgttl
    hmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevws
    pdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivgi
    htnysesqnwrglpryfnvtlrkrvvknp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4potB (B:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potB (B:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgtt
    lhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevw
    spdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivg
    ihtnysesqnwrglpryfnvtlrkrvvknp
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4potC (C:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potC (C:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlnemtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgttl
    hmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevws
    pdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivgi
    htnysesqnwrglpryfnvtlrkrvvknp
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4potD (D:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potD (D:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgtt
    lhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevw
    spdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivg
    ihtnysesqnwrglpryfnvtlrkrvvknp
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4potE (E:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potE (E:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlndmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgttl
    hmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevws
    pdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivgi
    htnysesqnwrglpryfnvtlrkrvvknp
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4potF (F:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potF (F:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgtt
    lhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevw
    spdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivg
    ihtnysesqnwrglpryfnvtlrkrvvknpyp
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4potG (G:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potG (G:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgtt
    lhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevw
    spdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivg
    ihtnysesqnwrglpryfnvtlrkrvvknp
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >4potH (H:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potH (H:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgtt
    lhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevw
    spdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivg
    ihtnysesqnwrglpryfnvtlrkrvvknp
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >4potI (I:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potI (I:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlndmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgttl
    hmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevws
    pdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivgi
    htnysesqnwrglpryfnvtlrkrvvknp
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >4potJ (J:)
    gshmggvevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnat
    tlptysvaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgti
    pvqgttlhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgk
    ypvevwspdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    avdivgihtnysesqnwrglpryfnvtlrkrvvknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4potJ (J:)
    vevlevrtgpdaitqieaylnprmgnnnptdelygysadinvasskasdnpnattlptys
    vaviklpmlnedmtcdtllmweavsvktevmgisslvnlhqggkyiygsssgtipvqgtt
    lhmfsvggeplelqglvasstttyptdmvtiknmkpvnqaldpnakalldkdgkypvevw
    spdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsavdivg
    ihtnysesqnwrglpryfnvtlrkrvvknpyp