PDB entry 3nzj

View 3nzj on RCSB PDB site
Description: Crystal structure of yeast 20S proteasome in complex with ligand 2a
Class: hydrolase/hydrolase inhibitor
Keywords: ubiquitin, protein degradation, N-terminal nucleophilic hydrolase, 19S regulatory particle, ubiquitin-tagged substrates, cytosol, nucleus, hydrolase-hydrolase inhibitor complex
Deposited on 2010-07-16, released 2011-02-16
The last revision prior to the SCOPe 2.01 freeze date was dated 2011-02-16, with a file datestamp of 2011-02-11.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: 0.233
AEROSPACI score: 0.3 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '1':
    Compound: Proteasome component PRE4
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain '2':
    Compound: Proteasome component PRE3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzj2_
  • Chain '3':
    Compound: TMC-95A mimic ligand 2a
    Database cross-references and differences (RAF-indexed):
    • PDB 3NZJ (0-4)
  • Chain '4':
    Compound: TMC-95A mimic ligand 2a
    Database cross-references and differences (RAF-indexed):
    • PDB 3NZJ (0-4)
  • Chain 'A':
    Compound: Proteasome component Y7
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzja_
  • Chain 'B':
    Compound: Proteasome component Y13
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjb_
  • Chain 'C':
    Compound: Proteasome component PRE6
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjc_
  • Chain 'D':
    Compound: Proteasome component PUP2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Proteasome component PRE5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzje_
  • Chain 'F':
    Compound: Proteasome component C1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Proteasome component C7-alpha
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjg_
  • Chain 'H':
    Compound: Proteasome component PUP1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: Proteasome component PUP3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzji_
  • Chain 'J':
    Compound: Proteasome component C11
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjj_
  • Chain 'K':
    Compound: Proteasome component PRE2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: Proteasome component C5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjl_
  • Chain 'M':
    Compound: Proteasome component PRE4
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: Proteasome component PRE3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjn_
  • Chain 'O':
    Compound: Proteasome component Y7
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjo_
  • Chain 'P':
    Compound: Proteasome component Y13
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjp_
  • Chain 'Q':
    Compound: Proteasome component PRE6
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjq_
  • Chain 'R':
    Compound: Proteasome component PUP2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'S':
    Compound: Proteasome component PRE5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjs_
  • Chain 'T':
    Compound: Proteasome component C1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'U':
    Compound: Proteasome component C7-alpha
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzju_
  • Chain 'V':
    Compound: Proteasome component PUP1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'W':
    Compound: Proteasome component PUP3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjw_
  • Chain 'X':
    Compound: Proteasome component C11
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjx_
  • Chain 'Y':
    Compound: Proteasome component PRE2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Z':
    Compound: Proteasome component C5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3nzjz_
  • Heterogens: MES, HOH

PDB Chain Sequences:

  • Chain '1':
    No sequence available.

  • Chain '2':
    Sequence, based on SEQRES records: (download)
    >3nzj2 (2:)
    mngiqvdinrlkkgevslgtsimavtfkdgvilgadsrtttgayianrvtdkltrvhdki
    wccrsgsaadtqaiadivqyhlelytsqygtpstetaasvfkelcyenkdnltagiivag
    yddknkgevytiplggsvhklpyaiagsgstfiygycdknfrenmskeetvdfikhslsq
    aikwdgssggvirmvvltaagverlifypdeyeql
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzj2 (2:)
    tsimavtfkdgvilgadsrtttgayianrvtdkltrvhdkiwccrsgsaadtqaiadivq
    yhlelytsqygtpstetaasvfkelcyenkdnltagiivagyddknkgevytiplggsvh
    klpyaiagsgstfiygycdknfrenmskeetvdfikhslsqaikwdgssggvirmvvlta
    agverlifypdeyeql
    

  • Chain '3':
    No sequence available.

  • Chain '4':
    No sequence available.

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3nzjA (A:)
    mtdrysfslttfspsgklgqidyaltavkqgvtslgikatngvviatekksssplamset
    lskvslltpdigavysgmgpdyrvlvdksrkvahtsykriygeypptkllvsevakimqe
    atqsggvrpfgvslliaghdefngfslyqvdpsgsyfpwkataigkgsvaaktflekrwn
    deleledaihialltlkesvegefngdtielaiigdenpdllgytgiptdkgprfrklts
    qeindrleal
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3nzjB (B:)
    mgsrrydsrttifspegrlyqveyalesishagtaigimasdgivlaaerkvtstlleqd
    tsteklyklndkiavavagltadaeilintarihaqnylktynedipveilvrrlsdikq
    gytqhgglrpfgvsfiyagyddrygyqlytsnpsgnytgwkaisvgantsaaqtllqmdy
    kddmkvddaielalktlskttdssaltydrlefatirkgandgevyqkifkpqeikdilv
    ktgitkkdedeeadedmk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjB (B:)
    gsrrydsrttifspegrlyqveyalesishagtaigimasdgivlaaerkvtstlleqdt
    steklyklndkiavavagltadaeilintarihaqnylktynedipveilvrrlsdikqg
    ytqhgglrpfgvsfiyagyddrygyqlytsnpsgnytgwkaisvgantsaaqtllqmdyk
    ddmkvddaielalktlskttdssaltydrlefatirkgandgevyqkifkpqeikdilvk
    tgit
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3nzjC (C:)
    msgydralsifspdghifqveyaleavkrgtcavgvkgkncvvlgcerrstlklqdtrit
    pskvskidshvvlsfsglnadsriliekarveaqshrltledpvtveyltryvagvqqry
    tqsggvrpfgvstliagfdprddepklyqtepsgiysswsaqtigrnsktvrefleknyd
    rkeppatveecvkltvrsllevvqtgaknieitvvkpdsdivalsseeinqyvtqieqek
    qeqqeqdkkkksnh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjC (C:)
    gydralsifspdghifqveyaleavkrgtcavgvkgkncvvlgcerrstlklqdtritps
    kvskidshvvlsfsglnadsriliekarveaqshrltledpvtveyltryvagvqqrytq
    sggvrpfgvstliagfdprddepklyqtepsgiysswsaqtigrnsktvrefleknydrk
    eppatveecvkltvrsllevvqtgaknieitvvkpdsdivalsseeinqyvtqieqekqe
    q
    

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3nzjE (E:)
    mfrnnydgdtvtfsptgrlfqveyaleaikqgsvtvglrsnthavlvalkrnadelssyq
    kkiikcdehmglslaglapdarvlsnylrqqcnysslvfnrklaveraghllcdkaqknt
    qsyggrpygvglliigydksgahllefqpsgnvtelygtaigarsqgaktylertldtfi
    kidgnpdelikagveaisqslrdesltvdnlsiaivgkdtpftiydgeavakyi
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjE (E:)
    frnnydgdtvtfsptgrlfqveyaleaikqgsvtvglrsnthavlvalkrnadelssyqk
    kiikcdehmglslaglapdarvlsnylrqqcnysslvfnrklaveraghllcdkaqkntq
    syggrpygvglliigydksgahllefqpsgnvtelygtaigarsqgaktylertldtfik
    idgnpdelikagveaisqslrdesltvdnlsiaivgkdtpftiydgeavakyi
    

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3nzjG (G:)
    msgaaaasaagydrhitifspegrlyqveyafkatnqtninslavrgkdctvvisqkkvp
    dklldpttvsyifcisrtigmvvngpipdarnaalrakaeaaefrykygydmpcdvlakr
    manlsqiytqraymrplgviltfvsvdeelgpsiyktdpagyyvgykatatgpkqqeitt
    nlenhfkkskidhineeswekvvefaithmidalgtefskndlevgvatkdkfftlsaen
    ieerlvaiaeqd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjG (G:)
    agydrhitifspegrlyqveyafkatnqtninslavrgkdctvvisqkkvpdklldpttv
    syifcisrtigmvvngpipdarnaalrakaeaaefrykygydmpcdvlakrmanlsqiyt
    qraymrplgviltfvsvdeelgpsiyktdpagyyvgykatatgpkqqeittnlenhfkks
    kidhineeswekvvefaithmidalgtefskndlevgvatkdkfftlsaenieerlvaia
    eqd
    

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >3nzjI (I:)
    msdpssinggivvamtgkdcvaiacdlrlgsqslgvsnkfekifhyghvflgitglatdv
    ttlnemfryktnlyklkeeraiepetftqlvssslyerrfgpyfvgpvvaginsksgkpf
    iagfdligcideakdfivsgtasdqlfgmceslyepnlepedlfetisqallnaadrdal
    sgwgavvyiikkdevvkrylkmrqd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjI (I:)
    sdpssinggivvamtgkdcvaiacdlrlgsqslgvsnkfekifhyghvflgitglatdvt
    tlnemfryktnlyklkeeraiepetftqlvssslyerrfgpyfvgpvvaginsksgkpfi
    agfdligcideakdfivsgtasdqlfgmceslyepnlepedlfetisqallnaadrdals
    gwgavvyiikkdevvkrylkmrqd
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3nzjJ (J:)
    mdiilgirvqdsvilasskavtrgisvlkdsddktrqlsphtlmsfageagdtvqfaeyi
    qaniqlysiredyelspqavssfvrqelaksirsrrpyqvnvliggydkkknkpelyqid
    ylgtkvelpygahgysgfytfslldhhyrpdmtteegldllklcvqelekrmpmdfkgvi
    vkivdkdgirqvddfqaq
    

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >3nzjL (L:)
    matiaseysseasntpiehqfnpygdnggtilgiagedfavlagdtrnitdysinsryep
    kvfdcgdnivmsangfaadgdalvkrfknsvkwyhfdhndkklsinsaarniqhllygkr
    ffpyyvhtiiagldedgkgavysfdpvgsyereqcraggaaaslimpfldnqvnfknqye
    pgtngkvkkplkylsveeviklvrdsftsaterhiqvgdgleilivtkdgvrkefyelkr
    d
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjL (L:)
    qfnpygdnggtilgiagedfavlagdtrnitdysinsryepkvfdcgdnivmsangfaad
    gdalvkrfknsvkwyhfdhndkklsinsaarniqhllygkrffpyyvhtiiagldedgkg
    avysfdpvgsyereqcraggaaaslimpfldnqvnfknqyepgtngkvkkplkylsveev
    iklvrdsftsaterhiqvgdgleilivtkdgvrkefyelkrd
    

  • Chain 'M':
    No sequence available.

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >3nzjN (N:)
    mngiqvdinrlkkgevslgtsimavtfkdgvilgadsrtttgayianrvtdkltrvhdki
    wccrsgsaadtqaiadivqyhlelytsqygtpstetaasvfkelcyenkdnltagiivag
    yddknkgevytiplggsvhklpyaiagsgstfiygycdknfrenmskeetvdfikhslsq
    aikwdgssggvirmvvltaagverlifypdeyeql
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjN (N:)
    tsimavtfkdgvilgadsrtttgayianrvtdkltrvhdkiwccrsgsaadtqaiadivq
    yhlelytsqygtpstetaasvfkelcyenkdnltagiivagyddknkgevytiplggsvh
    klpyaiagsgstfiygycdknfrenmskeetvdfikhslsqaikwdgssggvirmvvlta
    agverlifypdeyeql
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3nzjO (O:)
    mtdrysfslttfspsgklgqidyaltavkqgvtslgikatngvviatekksssplamset
    lskvslltpdigavysgmgpdyrvlvdksrkvahtsykriygeypptkllvsevakimqe
    atqsggvrpfgvslliaghdefngfslyqvdpsgsyfpwkataigkgsvaaktflekrwn
    deleledaihialltlkesvegefngdtielaiigdenpdllgytgiptdkgprfrklts
    qeindrleal
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >3nzjP (P:)
    mgsrrydsrttifspegrlyqveyalesishagtaigimasdgivlaaerkvtstlleqd
    tsteklyklndkiavavagltadaeilintarihaqnylktynedipveilvrrlsdikq
    gytqhgglrpfgvsfiyagyddrygyqlytsnpsgnytgwkaisvgantsaaqtllqmdy
    kddmkvddaielalktlskttdssaltydrlefatirkgandgevyqkifkpqeikdilv
    ktgitkkdedeeadedmk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjP (P:)
    gsrrydsrttifspegrlyqveyalesishagtaigimasdgivlaaerkvtstlleqdt
    steklyklndkiavavagltadaeilintarihaqnylktynedipveilvrrlsdikqg
    ytqhgglrpfgvsfiyagyddrygyqlytsnpsgnytgwkaisvgantsaaqtllqmdyk
    ddmkvddaielalktlskttdssaltydrlefatirkgandgevyqkifkpqeikdilvk
    tgit
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >3nzjQ (Q:)
    msgydralsifspdghifqveyaleavkrgtcavgvkgkncvvlgcerrstlklqdtrit
    pskvskidshvvlsfsglnadsriliekarveaqshrltledpvtveyltryvagvqqry
    tqsggvrpfgvstliagfdprddepklyqtepsgiysswsaqtigrnsktvrefleknyd
    rkeppatveecvkltvrsllevvqtgaknieitvvkpdsdivalsseeinqyvtqieqek
    qeqqeqdkkkksnh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjQ (Q:)
    gydralsifspdghifqveyaleavkrgtcavgvkgkncvvlgcerrstlklqdtritps
    kvskidshvvlsfsglnadsriliekarveaqshrltledpvtveyltryvagvqqrytq
    sggvrpfgvstliagfdprddepklyqtepsgiysswsaqtigrnsktvrefleknydrk
    eppatveecvkltvrsllevvqtgaknieitvvkpdsdivalsseeinqyvtqieqekqe
    q
    

  • Chain 'R':
    No sequence available.

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >3nzjS (S:)
    mfrnnydgdtvtfsptgrlfqveyaleaikqgsvtvglrsnthavlvalkrnadelssyq
    kkiikcdehmglslaglapdarvlsnylrqqcnysslvfnrklaveraghllcdkaqknt
    qsyggrpygvglliigydksgahllefqpsgnvtelygtaigarsqgaktylertldtfi
    kidgnpdelikagveaisqslrdesltvdnlsiaivgkdtpftiydgeavakyi
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjS (S:)
    frnnydgdtvtfsptgrlfqveyaleaikqgsvtvglrsnthavlvalkrnadelssyqk
    kiikcdehmglslaglapdarvlsnylrqqcnysslvfnrklaveraghllcdkaqkntq
    syggrpygvglliigydksgahllefqpsgnvtelygtaigarsqgaktylertldtfik
    idgnpdelikagveaisqslrdesltvdnlsiaivgkdtpftiydgeavakyi
    

  • Chain 'T':
    No sequence available.

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >3nzjU (U:)
    msgaaaasaagydrhitifspegrlyqveyafkatnqtninslavrgkdctvvisqkkvp
    dklldpttvsyifcisrtigmvvngpipdarnaalrakaeaaefrykygydmpcdvlakr
    manlsqiytqraymrplgviltfvsvdeelgpsiyktdpagyyvgykatatgpkqqeitt
    nlenhfkkskidhineeswekvvefaithmidalgtefskndlevgvatkdkfftlsaen
    ieerlvaiaeqd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjU (U:)
    agydrhitifspegrlyqveyafkatnqtninslavrgkdctvvisqkkvpdklldpttv
    syifcisrtigmvvngpipdarnaalrakaeaaefrykygydmpcdvlakrmanlsqiyt
    qraymrplgviltfvsvdeelgpsiyktdpagyyvgykatatgpkqqeittnlenhfkks
    kidhineeswekvvefaithmidalgtefskndlevgvatkdkfftlsaenieerlvaia
    eqd
    

  • Chain 'V':
    No sequence available.

  • Chain 'W':
    Sequence, based on SEQRES records: (download)
    >3nzjW (W:)
    msdpssinggivvamtgkdcvaiacdlrlgsqslgvsnkfekifhyghvflgitglatdv
    ttlnemfryktnlyklkeeraiepetftqlvssslyerrfgpyfvgpvvaginsksgkpf
    iagfdligcideakdfivsgtasdqlfgmceslyepnlepedlfetisqallnaadrdal
    sgwgavvyiikkdevvkrylkmrqd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjW (W:)
    sdpssinggivvamtgkdcvaiacdlrlgsqslgvsnkfekifhyghvflgitglatdvt
    tlnemfryktnlyklkeeraiepetftqlvssslyerrfgpyfvgpvvaginsksgkpfi
    agfdligcideakdfivsgtasdqlfgmceslyepnlepedlfetisqallnaadrdals
    gwgavvyiikkdevvkrylkmrqd
    

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3nzjX (X:)
    mdiilgirvqdsvilasskavtrgisvlkdsddktrqlsphtlmsfageagdtvqfaeyi
    qaniqlysiredyelspqavssfvrqelaksirsrrpyqvnvliggydkkknkpelyqid
    ylgtkvelpygahgysgfytfslldhhyrpdmtteegldllklcvqelekrmpmdfkgvi
    vkivdkdgirqvddfqaq
    

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    Sequence, based on SEQRES records: (download)
    >3nzjZ (Z:)
    matiaseysseasntpiehqfnpygdnggtilgiagedfavlagdtrnitdysinsryep
    kvfdcgdnivmsangfaadgdalvkrfknsvkwyhfdhndkklsinsaarniqhllygkr
    ffpyyvhtiiagldedgkgavysfdpvgsyereqcraggaaaslimpfldnqvnfknqye
    pgtngkvkkplkylsveeviklvrdsftsaterhiqvgdgleilivtkdgvrkefyelkr
    d
    

    Sequence, based on observed residues (ATOM records): (download)
    >3nzjZ (Z:)
    qfnpygdnggtilgiagedfavlagdtrnitdysinsryepkvfdcgdnivmsangfaad
    gdalvkrfknsvkwyhfdhndkklsinsaarniqhllygkrffpyyvhtiiagldedgkg
    avysfdpvgsyereqcraggaaaslimpfldnqvnfknqyepgtngkvkkplkylsveev
    iklvrdsftsaterhiqvgdgleilivtkdgvrkefyelkrd