PDB entry 3kdn

View 3kdn on RCSB PDB site
Description: Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP
Class: lyase
Keywords: ribulose-1,5-bisphosphate carboxylase/oxygenase, Rubisco, Carbon dioxide fixation, Lyase, Magnesium, Metal-binding, Monooxygenase
Deposited on 2009-10-23, released 2010-10-06
The last revision prior to the SCOPe 2.06 freeze date was dated 2011-02-02, with a file datestamp of 2011-01-28.
Experiment type: XRAY
Resolution: 2.09 Å
R-factor: 0.215
AEROSPACI score: 0.4 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdna1, d3kdna2
  • Chain 'B':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdnb1, d3kdnb2
  • Chain 'C':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdnc1, d3kdnc2
  • Chain 'D':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdnd1, d3kdnd2
  • Chain 'E':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdne1, d3kdne2
  • Chain 'F':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdnf1, d3kdnf2
  • Chain 'G':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdng1, d3kdng2
  • Chain 'H':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdnh1, d3kdnh2
  • Chain 'I':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdni1, d3kdni2
  • Chain 'J':
    Compound: Ribulose bisphosphate carboxylase
    Species: Thermococcus kodakaraensis [TaxId:69014]
    Gene: rbcL, TK2290
    Database cross-references and differences (RAF-indexed):
    • Uniprot O93627 (Start-443)
      • engineered (325-329)
    Domains in SCOPe 2.06: d3kdnj1, d3kdnj2
  • Heterogens: MG, CAP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3kdnA (A:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnA (A:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyrl
    igidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3kdnB (B:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnB (B:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyrl
    igidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3kdnC (C:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnC (C:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyrl
    igidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3kdnD (D:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnD (D:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyrl
    igidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3kdnE (E:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnE (E:)
    tiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqer
    wadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledl
    yfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngad
    ymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevlad
    lglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyr
    ligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafpts
    sgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyak
    thkelaralekwghvtpv
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3kdnF (F:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnF (F:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyrl
    igidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3kdnG (G:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnG (G:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyrl
    igidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3kdnH (H:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnH (H:)
    tiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqer
    wadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledl
    yfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngad
    ymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevlad
    lglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyr
    ligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafpts
    sgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyak
    thkelaralekwghvtpv
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >3kdnI (I:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnI (I:)
    ydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerwa
    dlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledlyf
    peklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngadym
    kddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladlg
    lkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyrli
    gidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafptssg
    glhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakth
    kelaralekwghvtpv
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >3kdnJ (J:)
    mvekfdtiydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlyp
    wyeqerwadlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkg
    lrledlyfpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydl
    lsngadymkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqr
    levladlglkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfv
    laklyrligidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysik
    aafptssgglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgip
    ldeyakthkelaralekwghvtpv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kdnJ (J:)
    iydyyvdkgyepskkrdiiavfrvtpaegytieqaagavaaesstgtwttlypwyeqerw
    adlsakaydfhdmgdgswivriaypfhafeeanlpgllasiagnifgmkrvkglrledly
    fpeklirefdgpafgiegvrkmleikdrpiygvvpkpkvgyspeefeklaydllsngady
    mkddenltspwynrfeeraeimakiidkvenetgekktwfanitadllemeqrlevladl
    glkhamvdvvitgwgalryirdlaadyglaihghramhaaftrnpyhgismfvlaklyrl
    igidqlhvgtagagklegerditiqnarilreshykpdendvfhleqkfysikaafptss
    gglhpgniqpviealgtdivlqlgggtlghpdgpaagaravrqaidaimqgipldeyakt
    hkelaralekwghvtpv