PDB entry 3dy4

View 3dy4 on RCSB PDB site
Description: Crystal structure of yeast 20S proteasome in complex with spirolactacystin
Class: hydrolase
Keywords: Proteasome, Inhibitor, Protein Degradation, Ubiquitin-Proteasome-Pathway, Hydrolase, Nucleus, Protease, Threonine protease, Phosphoprotein, Zymogen
Deposited on 2008-07-25, released 2008-11-04
The last revision prior to the SCOPe 2.08 freeze date was dated 2014-08-13, with a file datestamp of 2014-08-08.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.227
AEROSPACI score: 0.18 (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): Domains in SCOPe 2.08: d3dy41_
  • Chain '2':
    Compound: Proteasome component PRE3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy42_
  • Chain 'A':
    Compound: Proteasome component Y7
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4a_
  • Chain 'B':
    Compound: Proteasome component Y13
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4b_
  • Chain 'C':
    Compound: Proteasome component PRE6
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4c_
  • Chain 'D':
    Compound: Proteasome component PUP2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4d_
  • Chain 'E':
    Compound: Proteasome component PRE5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4e_
  • Chain 'F':
    Compound: Proteasome component C1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4f_
  • Chain 'G':
    Compound: Proteasome component C7-alpha
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4g_
  • Chain 'H':
    Compound: Proteasome component PUP1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4h_
  • Chain 'I':
    Compound: Proteasome component PUP3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4i_
  • Chain 'J':
    Compound: Proteasome component C11
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4j_
  • Chain 'K':
    Compound: Proteasome component PRE2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4k_
  • Chain 'L':
    Compound: Proteasome component C5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4l_
  • Chain 'M':
    Compound: Proteasome component PRE4
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4m_
  • Chain 'N':
    Compound: Proteasome component PRE3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4n_
  • Chain 'O':
    Compound: Proteasome component Y7
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4o_
  • Chain 'P':
    Compound: Proteasome component Y13
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4p_
  • Chain 'Q':
    Compound: Proteasome component PRE6
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4q_
  • Chain 'R':
    Compound: Proteasome component PUP2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4r_
  • Chain 'S':
    Compound: Proteasome component PRE5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4s_
  • Chain 'T':
    Compound: Proteasome component C1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4t_
  • Chain 'U':
    Compound: Proteasome component C7-alpha
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4u_
  • Chain 'V':
    Compound: Proteasome component PUP1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4v_
  • Chain 'W':
    Compound: Proteasome component PUP3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4w_
  • Chain 'X':
    Compound: Proteasome component C11
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4x_
  • Chain 'Y':
    Compound: Proteasome component PRE2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4y_
  • Chain 'Z':
    Compound: Proteasome component C5
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dy4z_
  • Heterogens: SLA, HOH

PDB Chain Sequences:

  • Chain '1':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy41 (1:)
tqqpivtgtsvismkydngviiaadnlgsygsllrfngverlipvgdntvvgisgdisdm
qhierllkdlvtenaydnpladaeealepsyifeylatvmyqrrskmnplwnaiivagvq
sngdqflryvnllgvtyssptlatgfgahmanpllrkvvdresdipkttvqvaeeaivna
mrvlyyrdarssrnfslaiidkntgltfkknlqvenmkwdfakdikgygtqki

  • Chain '2':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy42 (2:)
tsimavtfkdgvilgadsrtttgayianrvtdkltrvhdkiwccrsgsaadtqaiadivq
yhlelytsqygtpstetaasvfkelcyenkdnltagiivagyddknkgevytiplggsvh
klpyaiagsgstfiygycdknfrenmskeetvdfikhslsqaikwdgssggvirmvvlta
agverlifypdeyeql

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4A (A:)
mtdrysfslttfspsgklgqidyaltavkqgvtslgikatngvviatekksssplamset
lskvslltpdigavysgmgpdyrvlvdksrkvahtsykriygeypptkllvsevakimqe
atqsggvrpfgvslliaghdefngfslyqvdpsgsyfpwkataigkgsvaaktflekrwn
deleledaihialltlkesvegefngdtielaiigdenpdllgytgiptdkgprfrklts
qeindrleal

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4B (B:)
gsrrydsrttifspegrlyqveyalesishagtaigimasdgivlaaerkvtstlleqdt
steklyklndkiavavagltadaeilintarihaqnylktynedipveilvrrlsdikqg
ytqhgglrpfgvsfiyagyddrygyqlytsnpsgnytgwkaisvgantsaaqtllqmdyk
ddmkvddaielalktlskttdssaltydrlefatirkgandgevyqkifkpqeikdilvk
tgit

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4C (C:)
gydralsifspdghifqveyaleavkrgtcavgvkgkncvvlgcerrstlklqdtritps
kvskidshvvlsfsglnadsriliekarveaqshrltledpvtveyltryvagvqqrytq
sggvrpfgvstliagfdprddepklyqtepsgiysswsaqtigrnsktvrefleknydrk
eppatveecvkltvrsllevvqtgaknieitvvkpdsdivalsseeinqyvtqieqekqe
q

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4D (D:)
drgvstfspegrlfqveysleaiklgstaigiatkegvvlgvekratspllesdsiekiv
eidrhigcamsgltadarsmiehartaavthnlyydedinvesltqsvcdlalrfgegas
geerlmsrpfgvalliaghdaddgyqlfhaepsgtfyrynakaigsgsegaqaellnewh
ssltlkeaellvlkilkqvmeekldennaqlscitkqdgfkiydnektaelikelkekea
ae

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4E (E:)
frnnydgdtvtfsptgrlfqveyaleaikqgsvtvglrsnthavlvalkrnadelssyqk
kiikcdehmglslaglapdarvlsnylrqqcnysslvfnrklaveraghllcdkaqkntq
syggrpygvglliigydksgahllefqpsgnvtelygtaigarsqgaktylertldtfik
idgnpdelikagveaisqslrdesltvdnlsiaivgkdtpftiydgeavakyi

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4F (F:)
gtgydlsnsvfspdgrnfqveyavkavengttsigikcndgvvfaveklitskllvpqkn
vkiqvvdrhigcvysglipdgrhlvnrgreeaasfkklyktpipipafadrlgqyvqaht
lynsvrpfgvstifggvdkngahlymlepsgsywgykgaatgkgrqsakaeleklvdhhp
eglsareavkqaakiiylahednkekdfeleiswcslsetnglhkfvkgdllqeaidfaq
kein

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4G (G:)
agydrhitifspegrlyqveyafkatnqtninslavrgkdctvvisqkkvpdklldpttv
syifcisrtigmvvngpipdarnaalrakaeaaefrykygydmpcdvlakrmanlsqiyt
qraymrplgviltfvsvdeelgpsiyktdpagyyvgykatatgpkqqeittnlenhfkks
kidhineeswekvvefaithmidalgtefskndlevgvatkdkfftlsaenieerlvaia
eqd

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4H (H:)
ttivgvkfnngvviaadtrstqgpivadkncaklhrispkiwcagagtaadteavtqlig
snielhslytsreprvvsalqmlkqhlfkyqghigaylivagvdptgshlfsihahgstd
vgyylslgsgslaamavleshwkqdltkeeaiklasdaiqagiwndlgsgsnvdvcvmei
gkdaeylrnyltpnvreekqksykfprgttavlkesivnicd

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4I (I:)
sdpssinggivvamtgkdcvaiacdlrlgsqslgvsnkfekifhyghvflgitglatdvt
tlnemfryktnlyklkeeraiepetftqlvssslyerrfgpyfvgpvvaginsksgkpfi
agfdligcideakdfivsgtasdqlfgmceslyepnlepedlfetisqallnaadrdals
gwgavvyiikkdevvkrylkmrqd

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4J (J:)
mdiilgirvqdsvilasskavtrgisvlkdsddktrqlsphtlmsfageagdtvqfaeyi
qaniqlysiredyelspqavssfvrqelaksirsrrpyqvnvliggydkkknkpelyqid
ylgtkvelpygahgysgfytfslldhhyrpdmtteegldllklcvqelekrmpmdfkgvi
vkivdkdgirqvddfqaq

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4K (K:)
tttlafrfqggiivavdsratagnwvasqtvkkvieinpfllgtmaggaadcqfwetwlg
sqcrlhelrekerisvaaaskilsnlvyqykgaglsmgtmicgytrkegptiyyvdsdgt
rlkgdifcvgsgqtfaygvldsnykwdlsvedalylgkrsilaaahrdaysggsvnlyhv
tedgwiyhgnhdvgelfwkvkeeegsfnnvig

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4L (L:)
qfnpygdnggtilgiagedfavlagdtrnitdysinsryepkvfdcgdnivmsangfaad
gdalvkrfknsvkwyhfdhndkklsinsaarniqhllygkrffpyyvhtiiagldedgkg
avysfdpvgsyereqcraggaaaslimpfldnqvnfknqyepgtngkvkkplkylsveev
iklvrdsftsaterhiqvgdgleilivtkdgvrkefyelkrd

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4M (M:)
tqqpivtgtsvismkydngviiaadnlgsygsllrfngverlipvgdntvvgisgdisdm
qhierllkdlvtenaydnpladaeealepsyifeylatvmyqrrskmnplwnaiivagvq
sngdqflryvnllgvtyssptlatgfgahmanpllrkvvdresdipkttvqvaeeaivna
mrvlyyrdarssrnfslaiidkntgltfkknlqvenmkwdfakdikgygtqki

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4N (N:)
tsimavtfkdgvilgadsrtttgayianrvtdkltrvhdkiwccrsgsaadtqaiadivq
yhlelytsqygtpstetaasvfkelcyenkdnltagiivagyddknkgevytiplggsvh
klpyaiagsgstfiygycdknfrenmskeetvdfikhslsqaikwdgssggvirmvvlta
agverlifypdeyeql

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4O (O:)
mtdrysfslttfspsgklgqidyaltavkqgvtslgikatngvviatekksssplamset
lskvslltpdigavysgmgpdyrvlvdksrkvahtsykriygeypptkllvsevakimqe
atqsggvrpfgvslliaghdefngfslyqvdpsgsyfpwkataigkgsvaaktflekrwn
deleledaihialltlkesvegefngdtielaiigdenpdllgytgiptdkgprfrklts
qeindrleal

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4P (P:)
gsrrydsrttifspegrlyqveyalesishagtaigimasdgivlaaerkvtstlleqdt
steklyklndkiavavagltadaeilintarihaqnylktynedipveilvrrlsdikqg
ytqhgglrpfgvsfiyagyddrygyqlytsnpsgnytgwkaisvgantsaaqtllqmdyk
ddmkvddaielalktlskttdssaltydrlefatirkgandgevyqkifkpqeikdilvk
tgit

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4Q (Q:)
gydralsifspdghifqveyaleavkrgtcavgvkgkncvvlgcerrstlklqdtritps
kvskidshvvlsfsglnadsriliekarveaqshrltledpvtveyltryvagvqqrytq
sggvrpfgvstliagfdprddepklyqtepsgiysswsaqtigrnsktvrefleknydrk
eppatveecvkltvrsllevvqtgaknieitvvkpdsdivalsseeinqyvtqieqekqe
q

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4R (R:)
drgvstfspegrlfqveysleaiklgstaigiatkegvvlgvekratspllesdsiekiv
eidrhigcamsgltadarsmiehartaavthnlyydedinvesltqsvcdlalrfgegas
geerlmsrpfgvalliaghdaddgyqlfhaepsgtfyrynakaigsgsegaqaellnewh
ssltlkeaellvlkilkqvmeekldennaqlscitkqdgfkiydnektaelikelkekea
ae

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4S (S:)
frnnydgdtvtfsptgrlfqveyaleaikqgsvtvglrsnthavlvalkrnadelssyqk
kiikcdehmglslaglapdarvlsnylrqqcnysslvfnrklaveraghllcdkaqkntq
syggrpygvglliigydksgahllefqpsgnvtelygtaigarsqgaktylertldtfik
idgnpdelikagveaisqslrdesltvdnlsiaivgkdtpftiydgeavakyi

  • Chain 'T':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4T (T:)
gtgydlsnsvfspdgrnfqveyavkavengttsigikcndgvvfaveklitskllvpqkn
vkiqvvdrhigcvysglipdgrhlvnrgreeaasfkklyktpipipafadrlgqyvqaht
lynsvrpfgvstifggvdkngahlymlepsgsywgykgaatgkgrqsakaeleklvdhhp
eglsareavkqaakiiylahednkekdfeleiswcslsetnglhkfvkgdllqeaidfaq
kein

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4U (U:)
agydrhitifspegrlyqveyafkatnqtninslavrgkdctvvisqkkvpdklldpttv
syifcisrtigmvvngpipdarnaalrakaeaaefrykygydmpcdvlakrmanlsqiyt
qraymrplgviltfvsvdeelgpsiyktdpagyyvgykatatgpkqqeittnlenhfkks
kidhineeswekvvefaithmidalgtefskndlevgvatkdkfftlsaenieerlvaia
eqd

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4V (V:)
ttivgvkfnngvviaadtrstqgpivadkncaklhrispkiwcagagtaadteavtqlig
snielhslytsreprvvsalqmlkqhlfkyqghigaylivagvdptgshlfsihahgstd
vgyylslgsgslaamavleshwkqdltkeeaiklasdaiqagiwndlgsgsnvdvcvmei
gkdaeylrnyltpnvreekqksykfprgttavlkesivnicd

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4W (W:)
sdpssinggivvamtgkdcvaiacdlrlgsqslgvsnkfekifhyghvflgitglatdvt
tlnemfryktnlyklkeeraiepetftqlvssslyerrfgpyfvgpvvaginsksgkpfi
agfdligcideakdfivsgtasdqlfgmceslyepnlepedlfetisqallnaadrdals
gwgavvyiikkdevvkrylkmrqd

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4X (X:)
mdiilgirvqdsvilasskavtrgisvlkdsddktrqlsphtlmsfageagdtvqfaeyi
qaniqlysiredyelspqavssfvrqelaksirsrrpyqvnvliggydkkknkpelyqid
ylgtkvelpygahgysgfytfslldhhyrpdmtteegldllklcvqelekrmpmdfkgvi
vkivdkdgirqvddfqaq

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4Y (Y:)
tttlafrfqggiivavdsratagnwvasqtvkkvieinpfllgtmaggaadcqfwetwlg
sqcrlhelrekerisvaaaskilsnlvyqykgaglsmgtmicgytrkegptiyyvdsdgt
rlkgdifcvgsgqtfaygvldsnykwdlsvedalylgkrsilaaahrdaysggsvnlyhv
tedgwiyhgnhdvgelfwkvkeeegsfnnvig

  • Chain 'Z':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dy4Z (Z:)
qfnpygdnggtilgiagedfavlagdtrnitdysinsryepkvfdcgdnivmsangfaad
gdalvkrfknsvkwyhfdhndkklsinsaarniqhllygkrffpyyvhtiiagldedgkg
avysfdpvgsyereqcraggaaaslimpfldnqvnfknqyepgtngkvkkplkylsveev
iklvrdsftsaterhiqvgdgleilivtkdgvrkefyelkrd