PDB entry 1yi7

View 1yi7 on RCSB PDB site
Description: Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum
Class: hydrolase
Keywords: Beta-propeller, beta-sandwich, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, HYDROLASE
Deposited on 2005-01-11, released 2005-02-22
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-02-03, with a file datestamp of 2021-01-29.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: N/A
AEROSPACI score: 0.42 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Beta-xylosidase, family 43 glycosyl hydrolase
    Species: Clostridium acetobutylicum [TaxId:272562]
    Gene: CAC3452 (xynD)
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q97DM1 (3-533)
      • cloning artifact (1-2)
      • modified residue (63)
      • modified residue (97)
      • modified residue (143)
      • modified residue (444)
      • expression tag (534)
    Domains in SCOPe 2.08: d1yi7a1, d1yi7a2, d1yi7a3, d1yi7a4
  • Chain 'B':
    Compound: Beta-xylosidase, family 43 glycosyl hydrolase
    Species: Clostridium acetobutylicum [TaxId:272562]
    Gene: CAC3452 (xynD)
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q97DM1 (3-533)
      • cloning artifact (1-2)
      • modified residue (63)
      • modified residue (97)
      • modified residue (143)
      • modified residue (444)
      • expression tag (534)
    Domains in SCOPe 2.08: d1yi7b1, d1yi7b2, d1yi7b3, d1yi7b4
  • Chain 'C':
    Compound: Beta-xylosidase, family 43 glycosyl hydrolase
    Species: Clostridium acetobutylicum [TaxId:272562]
    Gene: CAC3452 (xynD)
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q97DM1 (3-533)
      • cloning artifact (1-2)
      • modified residue (63)
      • modified residue (97)
      • modified residue (143)
      • modified residue (444)
      • expression tag (534)
    Domains in SCOPe 2.08: d1yi7c1, d1yi7c2, d1yi7c3, d1yi7c4
  • Chain 'D':
    Compound: Beta-xylosidase, family 43 glycosyl hydrolase
    Species: Clostridium acetobutylicum [TaxId:272562]
    Gene: CAC3452 (xynD)
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q97DM1 (3-533)
      • cloning artifact (1-2)
      • modified residue (63)
      • modified residue (97)
      • modified residue (143)
      • modified residue (444)
      • expression tag (534)
    Domains in SCOPe 2.08: d1yi7d1, d1yi7d2, d1yi7d3, d1yi7d4
  • Heterogens: CA, SO4, EPE, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1yi7A (A:)
    msliknpilrgfnpdpsicradtdyyiatstfewfpgvqihhskdlvnwhlvahplnrts
    lldmkgnpnsggiwapdlsyhdgkfwliytdvkvtdgmwkdchnylttcesvdgvwsdpi
    tlngsgfdaslfhdndgkkylvnmywdqrtynhnfygivlqeysdkekkligkakiiykg
    tdikytegphiyhigdyyylftaeggttyehsetvarsknidgpyeidpeyplltswhdp
    rnslqkcghaslvhthtdewylahlvgrplpvgnqpvleqrgycplgretsiqriewvdn
    wprvvggkqgsvnveapkipevkwektydekdnfdsdklninfqslriplteniaslkak
    kgnlrlygkesltstftqafiarrwqsfkfdastsvsfspdtfqqaagltcyyntenwst
    iqvtwnedkgrvidivccdnfhfdmplksnvipipkdveyihlkvevrvetyqysysfdg
    inwskvpaifesrklsddyvqgggfftgafvginciditgnnkpadfdyfcykeeghhhh
    hh
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yi7A (A:)
    sliknpilrgfnpdpsicradtdyyiatstfewfpgvqihhskdlvnwhlvahplnrtsl
    ldmkgnpnsggiwapdlsyhdgkfwliytdvkvtdgmwkdchnylttcesvdgvwsdpit
    lngsgfdaslfhdndgkkylvnmywdqrtynhnfygivlqeysdkekkligkakiiykgt
    dikytegphiyhigdyyylftaeggttyehsetvarsknidgpyeidpeyplltswhdpr
    nslqkcghaslvhthtdewylahlvgrplpvgnqpvleqrgycplgretsiqriewvdnw
    prvvggkqgsvnveapkipevkwektydekdnfdsdklninfqslriplteniaslkakk
    gnlrlygkesltstftqafiarrwqsfkfdastsvsfspdtfqqaagltcyyntenwsti
    qvtwnedkgrvidivccdnfhfdmplksnvipipkdveyihlkvevrvetyqysysfdgi
    nwskvpaifesrklsddyvqgggfftgafvginciditgnnkpadfdyfcykee
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1yi7B (B:)
    msliknpilrgfnpdpsicradtdyyiatstfewfpgvqihhskdlvnwhlvahplnrts
    lldmkgnpnsggiwapdlsyhdgkfwliytdvkvtdgmwkdchnylttcesvdgvwsdpi
    tlngsgfdaslfhdndgkkylvnmywdqrtynhnfygivlqeysdkekkligkakiiykg
    tdikytegphiyhigdyyylftaeggttyehsetvarsknidgpyeidpeyplltswhdp
    rnslqkcghaslvhthtdewylahlvgrplpvgnqpvleqrgycplgretsiqriewvdn
    wprvvggkqgsvnveapkipevkwektydekdnfdsdklninfqslriplteniaslkak
    kgnlrlygkesltstftqafiarrwqsfkfdastsvsfspdtfqqaagltcyyntenwst
    iqvtwnedkgrvidivccdnfhfdmplksnvipipkdveyihlkvevrvetyqysysfdg
    inwskvpaifesrklsddyvqgggfftgafvginciditgnnkpadfdyfcykeeghhhh
    hh
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yi7B (B:)
    sliknpilrgfnpdpsicradtdyyiatstfewfpgvqihhskdlvnwhlvahplnrtsl
    ldmkgnpnsggiwapdlsyhdgkfwliytdvkvtdgmwkdchnylttcesvdgvwsdpit
    lngsgfdaslfhdndgkkylvnmywdqrtynhnfygivlqeysdkekkligkakiiykgt
    dikytegphiyhigdyyylftaeggttyehsetvarsknidgpyeidpeyplltswhdpr
    nslqkcghaslvhthtdewylahlvgrplpvgnqpvleqrgycplgretsiqriewvdnw
    prvvggkqgsvnveapkipevkwektydekdnfdsdklninfqslriplteniaslkakk
    gnlrlygkesltstftqafiarrwqsfkfdastsvsfspdtfqqaagltcyyntenwsti
    qvtwnedkgrvidivccdnfhfdmplksnvipipkdveyihlkvevrvetyqysysfdgi
    nwskvpaifesrklsddyvqgggfftgafvginciditgnnkpadfdyfcykee
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1yi7C (C:)
    msliknpilrgfnpdpsicradtdyyiatstfewfpgvqihhskdlvnwhlvahplnrts
    lldmkgnpnsggiwapdlsyhdgkfwliytdvkvtdgmwkdchnylttcesvdgvwsdpi
    tlngsgfdaslfhdndgkkylvnmywdqrtynhnfygivlqeysdkekkligkakiiykg
    tdikytegphiyhigdyyylftaeggttyehsetvarsknidgpyeidpeyplltswhdp
    rnslqkcghaslvhthtdewylahlvgrplpvgnqpvleqrgycplgretsiqriewvdn
    wprvvggkqgsvnveapkipevkwektydekdnfdsdklninfqslriplteniaslkak
    kgnlrlygkesltstftqafiarrwqsfkfdastsvsfspdtfqqaagltcyyntenwst
    iqvtwnedkgrvidivccdnfhfdmplksnvipipkdveyihlkvevrvetyqysysfdg
    inwskvpaifesrklsddyvqgggfftgafvginciditgnnkpadfdyfcykeeghhhh
    hh
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yi7C (C:)
    sliknpilrgfnpdpsicradtdyyiatstfewfpgvqihhskdlvnwhlvahplnrtsl
    ldmkgnpnsggiwapdlsyhdgkfwliytdvkvtdgmwkdchnylttcesvdgvwsdpit
    lngsgfdaslfhdndgkkylvnmywdqrtynhnfygivlqeysdkekkligkakiiykgt
    dikytegphiyhigdyyylftaeggttyehsetvarsknidgpyeidpeyplltswhdpr
    nslqkcghaslvhthtdewylahlvgrplpvgnqpvleqrgycplgretsiqriewvdnw
    prvvggkqgsvnveapkipevkwektydekdnfdsdklninfqslriplteniaslkakk
    gnlrlygkesltstftqafiarrwqsfkfdastsvsfspdtfqqaagltcyyntenwsti
    qvtwnedkgrvidivccdnfhfdmplksnvipipkdveyihlkvevrvetyqysysfdgi
    nwskvpaifesrklsddyvqgggfftgafvginciditgnnkpadfdyfcykee
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >1yi7D (D:)
    msliknpilrgfnpdpsicradtdyyiatstfewfpgvqihhskdlvnwhlvahplnrts
    lldmkgnpnsggiwapdlsyhdgkfwliytdvkvtdgmwkdchnylttcesvdgvwsdpi
    tlngsgfdaslfhdndgkkylvnmywdqrtynhnfygivlqeysdkekkligkakiiykg
    tdikytegphiyhigdyyylftaeggttyehsetvarsknidgpyeidpeyplltswhdp
    rnslqkcghaslvhthtdewylahlvgrplpvgnqpvleqrgycplgretsiqriewvdn
    wprvvggkqgsvnveapkipevkwektydekdnfdsdklninfqslriplteniaslkak
    kgnlrlygkesltstftqafiarrwqsfkfdastsvsfspdtfqqaagltcyyntenwst
    iqvtwnedkgrvidivccdnfhfdmplksnvipipkdveyihlkvevrvetyqysysfdg
    inwskvpaifesrklsddyvqgggfftgafvginciditgnnkpadfdyfcykeeghhhh
    hh
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yi7D (D:)
    sliknpilrgfnpdpsicradtdyyiatstfewfpgvqihhskdlvnwhlvahplnrtsl
    ldmkgnpnsggiwapdlsyhdgkfwliytdvkvtdgmwkdchnylttcesvdgvwsdpit
    lngsgfdaslfhdndgkkylvnmywdqrtynhnfygivlqeysdkekkligkakiiykgt
    dikytegphiyhigdyyylftaeggttyehsetvarsknidgpyeidpeyplltswhdpr
    nslqkcghaslvhthtdewylahlvgrplpvgnqpvleqrgycplgretsiqriewvdnw
    prvvggkqgsvnveapkipevkwektydekdnfdsdklninfqslriplteniaslkakk
    gnlrlygkesltstftqafiarrwqsfkfdastsvsfspdtfqqaagltcyyntenwsti
    qvtwnedkgrvidivccdnfhfdmplksnvipipkdveyihlkvevrvetyqysysfdgi
    nwskvpaifesrklsddyvqgggfftgafvginciditgnnkpadfdyfcykee