PDB entry 1upm

View 1upm on RCSB PDB site
Description: activated spinach rubisco complexed with 2-carboxyarabinitol 2 bisphosphat and ca2+.
Class: lyase
Keywords: lyase, carbon-carbon, oxidoreductase, photosynthesis, carbon-dioxide fixation lyase (carbon-carbon)
Deposited on 2003-10-08, released 2003-10-14
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.23
AEROSPACI score: 0.33 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'B':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1upmb1, d1upmb2
  • Chain 'C':
    Compound: ribulose bisphosphate carboxylase small chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q43832 (0-122)
      • conflict (1)
      • conflict (5-6)
      • conflict (8)
      • conflict (10)
      • conflict (108)
      • conflict (112)
    Domains in SCOPe 2.07: d1upmc_
  • Chain 'E':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1upme1, d1upme2
  • Chain 'F':
    Compound: ribulose bisphosphate carboxylase small chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q43832 (0-122)
      • conflict (1)
      • conflict (5-6)
      • conflict (8)
      • conflict (10)
      • conflict (108)
      • conflict (112)
    Domains in SCOPe 2.07: d1upmf_
  • Chain 'H':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1upmh1, d1upmh2
  • Chain 'I':
    Compound: ribulose bisphosphate carboxylase small chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q43832 (0-122)
      • conflict (1)
      • conflict (5-6)
      • conflict (8)
      • conflict (10)
      • conflict (108)
      • conflict (112)
    Domains in SCOPe 2.07: d1upmi_
  • Chain 'K':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1upmk1, d1upmk2
  • Chain 'L':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1upml1, d1upml2
  • Chain 'M':
    Compound: ribulose bisphosphate carboxylase small chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q43832 (0-122)
      • conflict (1)
      • conflict (5-6)
      • conflict (8)
      • conflict (10)
      • conflict (108)
      • conflict (112)
    Domains in SCOPe 2.07: d1upmm_
  • Chain 'O':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1upmo1, d1upmo2
  • Chain 'P':
    Compound: ribulose bisphosphate carboxylase small chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q43832 (0-122)
      • conflict (1)
      • conflict (5-6)
      • conflict (8)
      • conflict (10)
      • conflict (108)
      • conflict (112)
    Domains in SCOPe 2.07: d1upmp_
  • Chain 'R':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1upmr1, d1upmr2
  • Chain 'S':
    Compound: ribulose bisphosphate carboxylase small chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q43832 (0-122)
      • conflict (1)
      • conflict (5-6)
      • conflict (8)
      • conflict (10)
      • conflict (108)
      • conflict (112)
    Domains in SCOPe 2.07: d1upms_
  • Chain 'T':
    Compound: ribulose bisphosphate carboxylase small chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q43832 (0-122)
      • conflict (1)
      • conflict (5-6)
      • conflict (8)
      • conflict (10)
      • conflict (108)
      • conflict (112)
    Domains in SCOPe 2.07: d1upmt_
  • Chain 'V':
    Compound: ribulose bisphosphate carboxylase large chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1upmv1, d1upmv2
  • Chain 'W':
    Compound: ribulose bisphosphate carboxylase small chain
    Species: Spinacia oleracea [TaxId:3562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q43832 (0-122)
      • conflict (1)
      • conflict (5-6)
      • conflict (8)
      • conflict (10)
      • conflict (108)
      • conflict (112)
    Domains in SCOPe 2.07: d1upmw_
  • Heterogens: CA, CAP, HOH

PDB Chain Sequences:

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1upmB (B:)
    mspqtetkasvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaae
    sstgtwttvwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsi
    vgnvfgfkalralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghyl
    natagtcedmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhav
    idrqknhgmhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsr
    giyftqswvstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavan
    rvaleacvqarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

    Sequence, based on observed residues (ATOM records): (download)
    >1upmB (B:)
    asvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaaesstgtwtt
    vwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsivgnvfgfk
    alralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghylnatagtce
    dmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhavidrqknhg
    mhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsrgiyftqsw
    vstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavanrvaleacv
    qarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1upmC (C:)
    mqvwpilnlkkyetlsylpplttdqlarqvdyllnnkwvpclefetdhgfvyrehhnspg
    yydgrywtmwklpmfgctdpaqvlneleeckkeypnafiriigfdsnrevqcisfiaykp
    agy
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >1upmE (E:)
    mspqtetkasvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaae
    sstgtwttvwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsi
    vgnvfgfkalralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghyl
    natagtcedmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhav
    idrqknhgmhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsr
    giyftqswvstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavan
    rvaleacvqarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

    Sequence, based on observed residues (ATOM records): (download)
    >1upmE (E:)
    asvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaaesstgtwtt
    vwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsivgnvfgfk
    alralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghylnatagtce
    dmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhavidrqknhg
    mhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsrgiyftqsw
    vstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavanrvaleacv
    qarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1upmF (F:)
    mqvwpilnlkkyetlsylpplttdqlarqvdyllnnkwvpclefetdhgfvyrehhnspg
    yydgrywtmwklpmfgctdpaqvlneleeckkeypnafiriigfdsnrevqcisfiaykp
    agy
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >1upmH (H:)
    mspqtetkasvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaae
    sstgtwttvwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsi
    vgnvfgfkalralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghyl
    natagtcedmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhav
    idrqknhgmhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsr
    giyftqswvstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavan
    rvaleacvqarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

    Sequence, based on observed residues (ATOM records): (download)
    >1upmH (H:)
    asvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaaesstgtwtt
    vwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsivgnvfgfk
    alralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghylnatagtce
    dmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhavidrqknhg
    mhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsrgiyftqsw
    vstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavanrvaleacv
    qarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1upmI (I:)
    mqvwpilnlkkyetlsylpplttdqlarqvdyllnnkwvpclefetdhgfvyrehhnspg
    yydgrywtmwklpmfgctdpaqvlneleeckkeypnafiriigfdsnrevqcisfiaykp
    agy
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >1upmK (K:)
    mspqtetkasvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaae
    sstgtwttvwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsi
    vgnvfgfkalralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghyl
    natagtcedmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhav
    idrqknhgmhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsr
    giyftqswvstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavan
    rvaleacvqarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

    Sequence, based on observed residues (ATOM records): (download)
    >1upmK (K:)
    asvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaaesstgtwtt
    vwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsivgnvfgfk
    alralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghylnatagtce
    dmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhavidrqknhg
    mhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsrgiyftqsw
    vstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavanrvaleacv
    qarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >1upmL (L:)
    mspqtetkasvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaae
    sstgtwttvwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsi
    vgnvfgfkalralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghyl
    natagtcedmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhav
    idrqknhgmhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsr
    giyftqswvstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavan
    rvaleacvqarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

    Sequence, based on observed residues (ATOM records): (download)
    >1upmL (L:)
    asvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaaesstgtwtt
    vwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsivgnvfgfk
    alralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghylnatagtce
    dmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhavidrqknhg
    mhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsrgiyftqsw
    vstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavanrvaleacv
    qarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1upmM (M:)
    mqvwpilnlkkyetlsylpplttdqlarqvdyllnnkwvpclefetdhgfvyrehhnspg
    yydgrywtmwklpmfgctdpaqvlneleeckkeypnafiriigfdsnrevqcisfiaykp
    agy
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >1upmO (O:)
    mspqtetkasvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaae
    sstgtwttvwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsi
    vgnvfgfkalralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghyl
    natagtcedmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhav
    idrqknhgmhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsr
    giyftqswvstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavan
    rvaleacvqarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

    Sequence, based on observed residues (ATOM records): (download)
    >1upmO (O:)
    asvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaaesstgtwtt
    vwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsivgnvfgfk
    alralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghylnatagtce
    dmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhavidrqknhg
    mhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsrgiyftqsw
    vstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavanrvaleacv
    qarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1upmP (P:)
    mqvwpilnlkkyetlsylpplttdqlarqvdyllnnkwvpclefetdhgfvyrehhnspg
    yydgrywtmwklpmfgctdpaqvlneleeckkeypnafiriigfdsnrevqcisfiaykp
    agy
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >1upmR (R:)
    mspqtetkasvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaae
    sstgtwttvwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsi
    vgnvfgfkalralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghyl
    natagtcedmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhav
    idrqknhgmhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsr
    giyftqswvstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavan
    rvaleacvqarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

    Sequence, based on observed residues (ATOM records): (download)
    >1upmR (R:)
    asvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaaesstgtwtt
    vwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsivgnvfgfk
    alralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghylnatagtce
    dmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhavidrqknhg
    mhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsrgiyftqsw
    vstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavanrvaleacv
    qarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1upmS (S:)
    mqvwpilnlkkyetlsylpplttdqlarqvdyllnnkwvpclefetdhgfvyrehhnspg
    yydgrywtmwklpmfgctdpaqvlneleeckkeypnafiriigfdsnrevqcisfiaykp
    agy
    

  • Chain 'T':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1upmT (T:)
    mqvwpilnlkkyetlsylpplttdqlarqvdyllnnkwvpclefetdhgfvyrehhnspg
    yydgrywtmwklpmfgctdpaqvlneleeckkeypnafiriigfdsnrevqcisfiaykp
    agy
    

  • Chain 'V':
    Sequence, based on SEQRES records: (download)
    >1upmV (V:)
    mspqtetkasvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaae
    sstgtwttvwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsi
    vgnvfgfkalralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklgl
    saknygravyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghyl
    natagtcedmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhav
    idrqknhgmhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsr
    giyftqswvstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavan
    rvaleacvqarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

    Sequence, based on observed residues (ATOM records): (download)
    >1upmV (V:)
    asvefkagvkdykltyytpeyetldtdilaafrvspqpgvppeeagaavaaesstgtwtt
    vwtdgltnldrykgrcyhiepvageenqyicyvaypldlfeegsvtnmftsivgnvfgfk
    alralrledlripvayvktfqgpphgiqverdklnkygrpllgctikpklglsaknygra
    vyeclrggldftkddenvnsqpfmrwrdrflfcaealykaqaetgeikghylnatagtce
    dmmkravfarelgvpivmhdyltggftanttlshycrdnglllhihramhavidrqknhg
    mhfrvlakalrlsggdhihsgtvvgklegerditlgfvdllrddytekdrsrgiyftqsw
    vstpgvlpvasggihvwhmpalteifgddsvlqfgggtlghpwgnapgavanrvaleacv
    qarnegrdlaregntiireatkwspelaaacevwkeikfefpamdtv
    

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1upmW (W:)
    mqvwpilnlkkyetlsylpplttdqlarqvdyllnnkwvpclefetdhgfvyrehhnspg
    yydgrywtmwklpmfgctdpaqvlneleeckkeypnafiriigfdsnrevqcisfiaykp
    agy