PDB entry 5ipv

View 5ipv on RCSB PDB site
Description: cryo-em structure of glun1/glun2b nmda receptor in the dcka/d-apv- bound conformation, state 1
Deposited on 2016-03-10, released 2016-04-20
The last revision was dated 2016-05-04, with a file datestamp of 2016-04-29.
Experiment type: EM
Resolution: 9.25 Å
R-factor: N/A
AEROSPACI score: -0.14 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: N-methyl-D-aspartate receptor subunit NR1-8a
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0KD18 (0-End)
      • engineered mutation (28-29)
      • engineered mutation (277)
      • engineered mutation (327)
      • engineered mutation (345)
      • engineered mutation (417)
      • engineered mutation (446)
      • engineered mutation (470-472)
      • engineered mutation (738)
  • Chain 'B':
    Compound: Ionotropic glutamate receptor subunit NR2B
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot A7XY94
      • engineered mutation (63)
      • engineered mutation (68)
      • engineered mutation (342)
      • engineered mutation (485)
  • Chain 'C':
    Compound: N-methyl-D-aspartate receptor subunit NR1-8a
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0KD18 (0-End)
      • engineered mutation (28-29)
      • engineered mutation (277)
      • engineered mutation (327)
      • engineered mutation (345)
      • engineered mutation (417)
      • engineered mutation (446)
      • engineered mutation (470-472)
      • engineered mutation (738)
  • Chain 'D':
    Compound: Ionotropic glutamate receptor subunit NR2B
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot A7XY94
      • engineered mutation (63)
      • engineered mutation (68)
      • engineered mutation (342)
      • engineered mutation (485)

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.07, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >5ipvA (A:)
    dpkivnigavlstkkheqifreavnqanffhftrkiqlnatsvthrpnaiqmalsvcedl
    issqvyailvshppaptdhltptpisytagfyripviglttrmsiysdksihlsflrtvp
    pyshqalvwfemmrlfnwnhvilivsddhegraaqkkletlleekeskadkvlqfepgtk
    nltallleakelearviilsaseddatavyksaamldmtgagyvwlvgereisgsalrya
    pdgiiglqlingknesahisdavavvaqaihelfemeqitdpprgcvgntniwktgplfk
    rvlmsskypdgvtgriefnedgdrkfaqysimnlqnrklvqvgifdgsyiiqndrkiiwp
    ggeterpqgyqmstrlkivtihqepfvyvrpttsdgtcreeytingdpikkvicngpdet
    ipgrptvpqccygfcvdlliklaremdftyevhlvadgkfgtqervnnsnaaawngmmge
    llsgqadmivapltinneraqyiefskpfkyqgltilvkkeiprstldsfmqpfqstlwl
    lvglsvhvvavmlylldrfspfgrfedaltlssamwfswrvllnsglgegaprsfsaril
    gmvwagfamiivasytanlaaflvlrrpeeritgindprlrnpsdkfiyatvkqssvdiy
    frrqvelstmyrhmekhnyesaaeaiqavrdnklhafiwdsavlefeasqkcdlvttgel
    ffrsgfgigmrkdspwkqevslnilkshengfmeeldktwvryqecdsrsnapatltfen
    magvfmlvaggivagiflifieiayksraeakrmkglevlfq
    

    Sequence, based on observed residues (ATOM records):
    >5ipvA (A:)
    dpkivnigavlstkkheqifreavnqanffhftrkiqlnatsvthrpnaiqmalsvcedl
    issqvyailvshppaptdhltptpisytagfyripviglttrmsiysdksihlsflrtvp
    pyshqalvwfemmrlfnwnhvilivsddhegraaqkkletlleekeskadkvlqfepgtk
    nltallleakelearviilsaseddatavyksaamldmtgagyvwlvgereisgsalrya
    pdgiiglqlingknesahisdavavvaqaihelfemeqitdpprgcvgntniwktgplfk
    rvlmsskypdgvtgriefnedgdrkfaqysimnlqnrklvqvgifdgsyiiqndrkiiwp
    ggeteryqmstrlkivtihqepfvyvrpttsdgtcreeytingdpikkvicngpdetipg
    rptvpqccygfcvdlliklaremdftyevhlvadgkfgtqervnnsnaaawngmmgells
    gqadmivapltinneraqyiefskpfkyqgltilvkkitgindprlrnpsdkfiyatvkq
    ssvdiyfrrqvelstmyrhmekhnyesaaeaiqavrdnklhafiwdsavlefeasqkcdl
    vttgelffrsgfgigmrkdspwkqevslnilkshengfmeeldktwvryqecd
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >5ipvB (B:)
    mrpteaccylkisliilfysrayaqkhpnmdiavilvgtteevaikdvhekddfhhlpvt
    prvelvtmqesdpksiitricdlmsdkkvqgvvfgddtdqeaiaqildfisvqtltpilg
    ihggssmimadkeeasmffqfgpsieqqasvmlnimeeydwyifsivttyfpgyqdfenk
    vrstiensfvgweleevihldmslddidskiqnqlkklqspvillyctkeeatyifevah
    svgltgygftwivpslvagdtdtvpdefptglisvsydewdydlparvrdgiaiittaas
    tmlsehnsipqsksscnniqesrvyeahmlkrylinvtfegrdlsfsedgyqmhpklvii
    llnqerkwervgkykdrslkmwpvfdlypnseehkdehlsivtleeapfvivedvdplsg
    tcmrntvpcrkqirpenrteeggnyikrcckgfcidilkkiaktvkftydlylvtngkhg
    kkingvwngmigevvtkraymavgsltineersevvdfsvpfietgisvmvsrsngtvsp
    saflepfsadvwvmmfvmllivsavavfvfeyfspvgyngpsftigkaiwllwglvfnns
    lpvqnpkgttskimvsvwaffaviflasytanlaafmiqrryvdqvsglsdkkfqrpndf
    spafrfgtvpngsternirnnylemhsymvkfnqrsvqdallslksgkldafiydaavln
    ymagrdegcklvtigsgkvfattgygiaiqkdsgwkrqvdlailqlfgdgemeelealwl
    tgichneknevmssqldidnmagvfymlaaamalslitfimehlf
    

    Sequence, based on observed residues (ATOM records):
    >5ipvB (B:)
    mdiavilvgtteevaikdvhekddfhhlpvtprvelvtmqesdpksiitricdlmsdkkv
    qgvvfgddtdqeaiaqildfisvqtltpilgihggssmimadkeeasmffqfgpsieqqa
    svmlnimeeydwyifsivttyfpgyqdfenkvrstiensfvgweleevihldmslddids
    kiqnqlkklqspvillyctkeeatyifevahsvgltgygftwivpslvagdtdtvpdefp
    tglisvsydewdydlparvrdgiaiittaastmlsehnsipqsksscnniqesrvyeahm
    lkrylinvtfegrdlsfsedgyqmhpklviillnqerkwervgkykdrslkmwehlsivt
    leeapfvivedvdplsgtcmrntvpcrkqiikrcckgfcidilkkiaktvkftydlylvt
    ngkhgkkingvwngmigevvtkraymavgsltineersevvdfsvpfietgisvmvsrsq
    vsglsdkkfqrpndfspafrfgtvpngsternirnnylemhsymvkfnqrsvqdallslk
    sgkldafiydaavlnymagrdegcklvtigsgkvfattgygiaiqkdsgwkrqvdlailq
    lfgdgemeelealwltgichnek
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >5ipvC (C:)
    dpkivnigavlstkkheqifreavnqanffhftrkiqlnatsvthrpnaiqmalsvcedl
    issqvyailvshppaptdhltptpisytagfyripviglttrmsiysdksihlsflrtvp
    pyshqalvwfemmrlfnwnhvilivsddhegraaqkkletlleekeskadkvlqfepgtk
    nltallleakelearviilsaseddatavyksaamldmtgagyvwlvgereisgsalrya
    pdgiiglqlingknesahisdavavvaqaihelfemeqitdpprgcvgntniwktgplfk
    rvlmsskypdgvtgriefnedgdrkfaqysimnlqnrklvqvgifdgsyiiqndrkiiwp
    ggeterpqgyqmstrlkivtihqepfvyvrpttsdgtcreeytingdpikkvicngpdet
    ipgrptvpqccygfcvdlliklaremdftyevhlvadgkfgtqervnnsnaaawngmmge
    llsgqadmivapltinneraqyiefskpfkyqgltilvkkeiprstldsfmqpfqstlwl
    lvglsvhvvavmlylldrfspfgrfedaltlssamwfswrvllnsglgegaprsfsaril
    gmvwagfamiivasytanlaaflvlrrpeeritgindprlrnpsdkfiyatvkqssvdiy
    frrqvelstmyrhmekhnyesaaeaiqavrdnklhafiwdsavlefeasqkcdlvttgel
    ffrsgfgigmrkdspwkqevslnilkshengfmeeldktwvryqecdsrsnapatltfen
    magvfmlvaggivagiflifieiayksraeakrmkglevlfq
    

    Sequence, based on observed residues (ATOM records):
    >5ipvC (C:)
    dpkivnigavlstkkheqifreavnqanffhftrkiqlnatsvthrpnaiqmalsvcedl
    issqvyailvshppaptdhltptpisytagfyripviglttrmsiysdksihlsflrtvp
    pyshqalvwfemmrlfnwnhvilivsddhegraaqkkletlleekeskadkvlqfepgtk
    nltallleakelearviilsaseddatavyksaamldmtgagyvwlvgereisgsalrya
    pdgiiglqlingknesahisdavavvaqaihelfemeqitdpprgcvgntniwktgplfk
    rvlmsskypdgvtgriefnedgdrkfaqysimnlqnrklvqvgifdgsyiiqndrkiiwp
    ggeteryqmstrlkivtihqepfvyvrpttsdgtcreeytingdpikkvicngpdetipg
    rptvpqccygfcvdlliklaremdftyevhlvadgkfgtqervnnsnaaawngmmgells
    gqadmivapltinneraqyiefskpfkyqgltilvkkitgindprlrnpsdkfiyatvkq
    ssvdiyfrrqvelstmyrhmekhnyesaaeaiqavrdnklhafiwdsavlefeasqkcdl
    vttgelffrsgfgigmrkdspwkqevslnilkshengfmeeldktwvryqecd
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >5ipvD (D:)
    mrpteaccylkisliilfysrayaqkhpnmdiavilvgtteevaikdvhekddfhhlpvt
    prvelvtmqesdpksiitricdlmsdkkvqgvvfgddtdqeaiaqildfisvqtltpilg
    ihggssmimadkeeasmffqfgpsieqqasvmlnimeeydwyifsivttyfpgyqdfenk
    vrstiensfvgweleevihldmslddidskiqnqlkklqspvillyctkeeatyifevah
    svgltgygftwivpslvagdtdtvpdefptglisvsydewdydlparvrdgiaiittaas
    tmlsehnsipqsksscnniqesrvyeahmlkrylinvtfegrdlsfsedgyqmhpklvii
    llnqerkwervgkykdrslkmwpvfdlypnseehkdehlsivtleeapfvivedvdplsg
    tcmrntvpcrkqirpenrteeggnyikrcckgfcidilkkiaktvkftydlylvtngkhg
    kkingvwngmigevvtkraymavgsltineersevvdfsvpfietgisvmvsrsngtvsp
    saflepfsadvwvmmfvmllivsavavfvfeyfspvgyngpsftigkaiwllwglvfnns
    lpvqnpkgttskimvsvwaffaviflasytanlaafmiqrryvdqvsglsdkkfqrpndf
    spafrfgtvpngsternirnnylemhsymvkfnqrsvqdallslksgkldafiydaavln
    ymagrdegcklvtigsgkvfattgygiaiqkdsgwkrqvdlailqlfgdgemeelealwl
    tgichneknevmssqldidnmagvfymlaaamalslitfimehlf
    

    Sequence, based on observed residues (ATOM records):
    >5ipvD (D:)
    mdiavilvgtteevaikdvhekddfhhlpvtprvelvtmqesdpksiitricdlmsdkkv
    qgvvfgddtdqeaiaqildfisvqtltpilgihggssmimadkeeasmffqfgpsieqqa
    svmlnimeeydwyifsivttyfpgyqdfenkvrstiensfvgweleevihldmslddids
    kiqnqlkklqspvillyctkeeatyifevahsvgltgygftwivpslvagdtdtvpdefp
    tglisvsydewdydlparvrdgiaiittaastmlsehnsipqsksscnniqesrvyeahm
    lkrylinvtfegrdlsfsedgyqmhpklviillnqerkwervgkykdrslkmwehlsivt
    leeapfvivedvdplsgtcmrntvpcrkqiikrcckgfcidilkkiaktvkftydlylvt
    ngkhgkkingvwngmigevvtkraymavgsltineersevvdfsvpfietgisvmvsrqv
    sglsdkkfqrpndfspafrfgtvpngsternirnnylemhsymvkfnqrsvqdallslks
    gkldafiydaavlnymagrdegcklvtigsgkvfattgygiaiqkdsgwkrqvdlailql
    fgdgemeelealwltgichnek