PDB entry 3wqp

View 3wqp on RCSB PDB site
Description: Crystal structure of Rubisco T289D mutant from Thermococcus kodakarensis
Class: lyase
Keywords: decamer, protein-ligand complex, LYASE
Deposited on 2014-01-29, released 2015-02-04
The last revision prior to the SCOPe 2.06 freeze date was dated 2015-02-04, with a file datestamp of 2015-01-30.
Experiment type: XRAY
Resolution: 2.25 Å
R-factor: 0.222
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpa1, d3wqpa2
  • Chain 'B':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpb1, d3wqpb2
  • Chain 'C':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpc1, d3wqpc2
  • Chain 'D':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpd1, d3wqpd2
  • Chain 'E':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpe1, d3wqpe2
  • Chain 'F':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpf1, d3wqpf2
  • Chain 'G':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpg1, d3wqpg2
  • Chain 'H':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqph1, d3wqph2
  • Chain 'I':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpi1, d3wqpi2
  • Chain 'J':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakarensis [TaxId:69014]
    Gene: rbcL, rbc, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered mutation (288)
    Domains in SCOPe 2.06: d3wqpj1, d3wqpj2
  • Heterogens: MG, CAP, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3wqpA (A:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpA (A:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyrl
    igidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3wqpB (B:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpB (B:)
    tiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqer
    wadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledl
    yfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngad
    ymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevlad
    lglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyr
    ligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafpts
    sgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyak
    thkelaralekwghvtpv
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3wqpC (C:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpC (C:)
    tiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqer
    wadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledl
    yfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngad
    ymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevlad
    lglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyr
    ligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafpts
    sgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyak
    thkelaralekwghvtpv
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3wqpD (D:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpD (D:)
    ydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerwa
    dlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledlyf
    peklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngadym
    kddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladlg
    lkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyrli
    gidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafptssg
    glhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakth
    kelaralekwghvtpv
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3wqpE (E:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpE (E:)
    tiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqer
    wadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledl
    yfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngad
    ymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevlad
    lglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyr
    ligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafpts
    sgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyak
    thkelaralekwghvtpv
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3wqpF (F:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpF (F:)
    ydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerwa
    dlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledlyf
    peklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngadym
    kddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladlg
    lkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyrli
    gidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafptssg
    glhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakth
    kelaralekwghvtpv
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3wqpG (G:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpG (G:)
    ydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerwa
    dlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledlyf
    peklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngadym
    kddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladlg
    lkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyrli
    gidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafptssg
    glhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakth
    kelaralekwghvtpv
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3wqpH (H:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpH (H:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyrl
    igidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >3wqpI (I:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpI (I:)
    ydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerwa
    dlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledlyf
    peklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngadym
    kddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladlg
    lkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyrli
    gidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafptssg
    glhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakth
    kelaralekwghvtpv
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >3wqpJ (J:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfv
    laklyrligidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3wqpJ (J:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaafdrnpyhgismfvlaklyrl
    igidqlhvgtagagkleggkwdviqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv