PDB entry 5luc

View 5luc on RCSB PDB site
Description: Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.8 Angstrom; internal aldimine with PLP in the active site
Class: transferase
Keywords: Primary Hyperoxaluria Type I, PH1, Transferase
Deposited on 2016-09-08, released 2017-09-20
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-09-27, with a file datestamp of 2017-09-22.
Experiment type: XRAY
Resolution: 1.8 Å
R-factor: N/A
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Serine--pyruvate aminotransferase
    Species: Homo sapiens [TaxId:9606]
    Gene: AGXT, AGT1, SPAT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21549
      • engineered mutation (193)
    Domains in SCOPe 2.07: d5luca_
  • Chain 'B':
    Compound: Serine--pyruvate aminotransferase
    Species: Homo sapiens [TaxId:9606]
    Gene: AGXT, AGT1, SPAT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21549
      • engineered mutation (193)
    Domains in SCOPe 2.07: d5lucb_
  • Chain 'E':
    Compound: Serine--pyruvate aminotransferase
    Species: Homo sapiens [TaxId:9606]
    Gene: AGXT, AGT1, SPAT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21549
      • engineered mutation (193)
    Domains in SCOPe 2.07: d5luce_
  • Chain 'G':
    Compound: Serine--pyruvate aminotransferase
    Species: Homo sapiens [TaxId:9606]
    Gene: AGXT, AGT1, SPAT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21549
      • engineered mutation (193)
    Domains in SCOPe 2.07: d5lucg_
  • Chain 'M':
    Compound: Serine--pyruvate aminotransferase
    Species: Homo sapiens [TaxId:9606]
    Gene: AGXT, AGT1, SPAT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21549
      • engineered mutation (193)
    Domains in SCOPe 2.07: d5lucm_
  • Chain 'N':
    Compound: Serine--pyruvate aminotransferase
    Species: Homo sapiens [TaxId:9606]
    Gene: AGXT, AGT1, SPAT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21549
      • engineered mutation (193)
    Domains in SCOPe 2.07: d5lucn_
  • Chain 'S':
    Compound: Serine--pyruvate aminotransferase
    Species: Homo sapiens [TaxId:9606]
    Gene: AGXT, AGT1, SPAT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21549
      • engineered mutation (193)
    Domains in SCOPe 2.07: d5lucs_
  • Chain 'T':
    Compound: Serine--pyruvate aminotransferase
    Species: Homo sapiens [TaxId:9606]
    Gene: AGXT, AGT1, SPAT
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21549
      • engineered mutation (193)
    Domains in SCOPe 2.07: d5luct_
  • Heterogens: PLP, BTB, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5lucA (A:)
    mggshhhhhhgmashkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsm
    skdmyqimdeikegiqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwg
    qravdigerigarvhpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgf
    gelchrykclllvnsvaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkk
    mysrktkpfsfyldikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswr
    qhreaaaylhgrlqalglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimg
    glgpstgkvlrigllgcnatrenvdrvtealraalqhcpkkkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5lucA (A:)
    hkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsmskdmyqimdeikeg
    iqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwgqravdigerigarv
    hpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgfgelchrykclllvn
    svaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkkmysrktkpfsfyld
    ikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswrqhreaaaylhgrlq
    alglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimgglgpstgkvlrigl
    lgcnatrenvdrvtealraalqhcpkk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5lucB (B:)
    mggshhhhhhgmashkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsm
    skdmyqimdeikegiqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwg
    qravdigerigarvhpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgf
    gelchrykclllvnsvaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkk
    mysrktkpfsfyldikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswr
    qhreaaaylhgrlqalglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimg
    glgpstgkvlrigllgcnatrenvdrvtealraalqhcpkkkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5lucB (B:)
    kllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsmskdmyqimdeikegi
    qyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwgqravdigerigarvh
    pmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgfgelchrykclllvns
    vaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkkmysrktkpfsfyldi
    kwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswrqhreaaaylhgrlqa
    lglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimgglgpstgkvlrigll
    gcnatrenvdrvtealraalqhcpkk
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5lucE (E:)
    mggshhhhhhgmashkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsm
    skdmyqimdeikegiqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwg
    qravdigerigarvhpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgf
    gelchrykclllvnsvaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkk
    mysrktkpfsfyldikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswr
    qhreaaaylhgrlqalglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimg
    glgpstgkvlrigllgcnatrenvdrvtealraalqhcpkkkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5lucE (E:)
    kllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsmskdmyqimdeikegi
    qyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwgqravdigerigarvh
    pmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgfgelchrykclllvns
    vaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkkmysrktkpfsfyldi
    kwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswrqhreaaaylhgrlqa
    lglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimgglgpstgkvlrigll
    gcnatrenvdrvtealraalqhcpkk
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5lucG (G:)
    mggshhhhhhgmashkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsm
    skdmyqimdeikegiqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwg
    qravdigerigarvhpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgf
    gelchrykclllvnsvaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkk
    mysrktkpfsfyldikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswr
    qhreaaaylhgrlqalglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimg
    glgpstgkvlrigllgcnatrenvdrvtealraalqhcpkkkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5lucG (G:)
    kllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsmskdmyqimdeikegi
    qyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwgqravdigerigarvh
    pmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgfgelchrykclllvns
    vaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkkmysrktkpfsfyldi
    kwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswrqhreaaaylhgrlqa
    lglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimgglgpstgkvlrigll
    gcnatrenvdrvtealraalqhcpkk
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >5lucM (M:)
    mggshhhhhhgmashkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsm
    skdmyqimdeikegiqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwg
    qravdigerigarvhpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgf
    gelchrykclllvnsvaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkk
    mysrktkpfsfyldikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswr
    qhreaaaylhgrlqalglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimg
    glgpstgkvlrigllgcnatrenvdrvtealraalqhcpkkkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5lucM (M:)
    kllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsmskdmyqimdeikegi
    qyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwgqravdigerigarvh
    pmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgfgelchrykclllvns
    vaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkkmysrktkpfsfyldi
    kwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswrqhreaaaylhgrlqa
    lglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimgglgpstgkvlrigll
    gcnatrenvdrvtealraalqhcpkk
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >5lucN (N:)
    mggshhhhhhgmashkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsm
    skdmyqimdeikegiqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwg
    qravdigerigarvhpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgf
    gelchrykclllvnsvaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkk
    mysrktkpfsfyldikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswr
    qhreaaaylhgrlqalglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimg
    glgpstgkvlrigllgcnatrenvdrvtealraalqhcpkkkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5lucN (N:)
    hkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsmskdmyqimdeikeg
    iqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwgqravdigerigarv
    hpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgfgelchrykclllvn
    svaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkkmysrktkpfsfyld
    ikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswrqhreaaaylhgrlq
    alglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimgglgpstgkvlrigl
    lgcnatrenvdrvtealraalqhcpkk
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >5lucS (S:)
    mggshhhhhhgmashkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsm
    skdmyqimdeikegiqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwg
    qravdigerigarvhpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgf
    gelchrykclllvnsvaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkk
    mysrktkpfsfyldikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswr
    qhreaaaylhgrlqalglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimg
    glgpstgkvlrigllgcnatrenvdrvtealraalqhcpkkkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5lucS (S:)
    kllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsmskdmyqimdeikegi
    qyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwgqravdigerigarvh
    pmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgfgelchrykclllvns
    vaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkkmysrktkpfsfyldi
    kwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswrqhreaaaylhgrlqa
    lglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimgglgpstgkvlrigll
    gcnatrenvdrvtealraalqhcpkk
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >5lucT (T:)
    mggshhhhhhgmashkllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsm
    skdmyqimdeikegiqyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwg
    qravdigerigarvhpmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgf
    gelchrykclllvnsvaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkk
    mysrktkpfsfyldikwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswr
    qhreaaaylhgrlqalglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimg
    glgpstgkvlrigllgcnatrenvdrvtealraalqhcpkkkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5lucT (T:)
    kllvtppkallkplsipnqlllgpgpsnlpprimaagglqmigsmskdmyqimdeikegi
    qyvfqtrnpltlvisgsghcaleaalvnvlepgdsflvgangiwgqravdigerigarvh
    pmtkdpgghytlqeveeglaqhkpvllflthgesstgvlqpldgfgelchrykclllvns
    vaslggtplymdrqgidilysgsqkalnappgtslisfsdkakkkmysrktkpfsfyldi
    kwlanfwgcddqprmyhhtipvislyslreslaliaeqglenswrqhreaaaylhgrlqa
    lglqlfvkdpalrlptvttvavpagydwrdivsyvidhfdieimgglgpstgkvlrigll
    gcnatrenvdrvtealraalqhcpkk