PDB entry 4d8y

View 4d8y on RCSB PDB site
Description: Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in space group P212121 at pH 5.6
Class: transferase
Keywords: Phosphorylase/hydrolase-like, TRANSFERASE
Deposited on 2012-01-11, released 2012-09-26
The last revision prior to the SCOPe 2.08 freeze date was dated 2012-09-26, with a file datestamp of 2012-09-21.
Experiment type: XRAY
Resolution: 1.61 Å
R-factor: 0.167
AEROSPACI score: 0.6 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Purine nucleoside phosphorylase deoD-type
    Species: Bacillus subtilis [TaxId:1423]
    Gene: BSU19630, deoD, punB
    Database cross-references and differences (RAF-indexed):
    • Uniprot O34925 (20-End)
      • expression tag (12-19)
      • see remark 999 (244)
    Domains in SCOPe 2.08: d4d8ya1, d4d8ya2
  • Chain 'B':
    Compound: Purine nucleoside phosphorylase deoD-type
    Species: Bacillus subtilis [TaxId:1423]
    Gene: BSU19630, deoD, punB
    Database cross-references and differences (RAF-indexed):
    • Uniprot O34925 (20-End)
      • expression tag (12-19)
      • see remark 999 (244)
    Domains in SCOPe 2.08: d4d8yb1, d4d8yb2
  • Chain 'C':
    Compound: Purine nucleoside phosphorylase deoD-type
    Species: Bacillus subtilis [TaxId:1423]
    Gene: BSU19630, deoD, punB
    Database cross-references and differences (RAF-indexed):
    • Uniprot O34925 (20-End)
      • expression tag (12-19)
      • see remark 999 (244)
    Domains in SCOPe 2.08: d4d8yc1, d4d8yc2
  • Chain 'D':
    Compound: Purine nucleoside phosphorylase deoD-type
    Species: Bacillus subtilis [TaxId:1423]
    Gene: BSU19630, deoD, punB
    Database cross-references and differences (RAF-indexed):
    • Uniprot O34925 (20-End)
      • expression tag (12-19)
      • see remark 999 (244)
    Domains in SCOPe 2.08: d4d8yd1, d4d8yd2
  • Chain 'E':
    Compound: Purine nucleoside phosphorylase deoD-type
    Species: Bacillus subtilis [TaxId:1423]
    Gene: BSU19630, deoD, punB
    Database cross-references and differences (RAF-indexed):
    • Uniprot O34925 (20-End)
      • expression tag (12-19)
      • see remark 999 (244)
    Domains in SCOPe 2.08: d4d8ye1, d4d8ye2
  • Chain 'F':
    Compound: Purine nucleoside phosphorylase deoD-type
    Species: Bacillus subtilis [TaxId:1423]
    Gene: BSU19630, deoD, punB
    Database cross-references and differences (RAF-indexed):
    • Uniprot O34925 (20-End)
      • expression tag (12-19)
      • see remark 999 (244)
    Domains in SCOPe 2.08: d4d8yf1, d4d8yf2
  • Heterogens: SO4, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4d8yA (A:)
    mgsshhhhhhssglvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecyn
    evrgmygftgtykgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkv
    rdvilamtsstdsqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfy
    nddsqieklakygvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttf
    hdmidvalhsvsq
    

    Sequence, based on observed residues (ATOM records): (download)
    >4d8yA (A:)
    glvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecynevrgmygftgty
    kgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkvrdvilamtsstd
    sqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfynddsqieklaky
    gvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttfhdmidvalhsvs
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4d8yB (B:)
    mgsshhhhhhssglvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecyn
    evrgmygftgtykgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkv
    rdvilamtsstdsqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfy
    nddsqieklakygvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttf
    hdmidvalhsvsq
    

    Sequence, based on observed residues (ATOM records): (download)
    >4d8yB (B:)
    glvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecynevrgmygftgty
    kgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkvrdvilamtsstd
    sqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfynddsqieklaky
    gvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttfhdmidvalhsvs
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4d8yC (C:)
    mgsshhhhhhssglvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecyn
    evrgmygftgtykgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkv
    rdvilamtsstdsqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfy
    nddsqieklakygvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttf
    hdmidvalhsvsq
    

    Sequence, based on observed residues (ATOM records): (download)
    >4d8yC (C:)
    glvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecynevrgmygftgty
    kgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkvrdvilamtsstd
    sqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfynddsqieklaky
    gvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttfhdmidvalhsvs
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4d8yD (D:)
    mgsshhhhhhssglvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecyn
    evrgmygftgtykgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkv
    rdvilamtsstdsqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfy
    nddsqieklakygvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttf
    hdmidvalhsvsq
    

    Sequence, based on observed residues (ATOM records): (download)
    >4d8yD (D:)
    glvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecynevrgmygftgty
    kgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkvrdvilamtsstd
    sqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfynddsqieklaky
    gvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttfhdmidvalhsvs
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4d8yE (E:)
    mgsshhhhhhssglvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecyn
    evrgmygftgtykgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkv
    rdvilamtsstdsqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfy
    nddsqieklakygvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttf
    hdmidvalhsvsq
    

    Sequence, based on observed residues (ATOM records): (download)
    >4d8yE (E:)
    glvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecynevrgmygftgty
    kgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkvrdvilamtsstd
    sqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfynddsqieklaky
    gvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttfhdmidvalhsvs
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4d8yF (F:)
    mgsshhhhhhssglvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecyn
    evrgmygftgtykgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkv
    rdvilamtsstdsqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfy
    nddsqieklakygvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttf
    hdmidvalhsvsq
    

    Sequence, based on observed residues (ATOM records): (download)
    >4d8yF (F:)
    glvprgshmsvhigaekgqiadtvllpgdplrakfiaetylenvecynevrgmygftgty
    kgkkisvqgtgmgvpsisiyvneliqsydvqnlirvgscgairkdvkvrdvilamtsstd
    sqmnrvafgsvdfapcadfellknaydaakdkgvpvtvgsvftadqfynddsqieklaky
    gvlgvemettalytlaakhgrkalsiltvsdhvltgeettaeerqttfhdmidvalhsvs