PDB entry 6z6p

View 6z6p on RCSB PDB site
Description: hdac-pc-nuc
Deposited on 2020-05-28, released 2021-02-17
The last revision was dated 2021-02-17, with a file datestamp of 2021-02-12.
Experiment type: EM
Resolution: 4.43 Å
R-factor: N/A
AEROSPACI score: 0.08 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: histone h3
    Species: Xenopus laevis [TaxId:8355]
    Gene: XELAEV_18002543mg
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: histone h2a
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h2aj, h2ac14, LOC494591, XELAEV_18003602mg
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: histone h2b
    Species: Xenopus laevis [TaxId:8355]
    Gene: XELAEV_18032685mg
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Histone H3.2
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84233 (0-96)
      • conflict (63)
  • Chain 'F':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Histone H2A type 1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06897 (0-104)
      • conflict (85)
  • Chain 'H':
    Compound: histone h2b
    Species: Xenopus laevis [TaxId:8355]
    Gene: XELAEV_18032686mg
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: DNA (145-mer)
    Species: unidentified plasmid, synthetic [TaxId:45202]
  • Chain 'J':
    Compound: DNA (145-mer)
    Species: unidentified plasmid, synthetic [TaxId:45202]
  • Chain 'K':
    Compound: Histone deacetylase HDA1
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: HDA1, YNL021W, N2819
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: Histone deacetylase HDA1
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: HDA1, YNL021W, N2819
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: HDA1 complex subunit 3,HDA1 complex subunit 3
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: HDA3, PLO1, YPR179C
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: HDA1 complex subunit 2
    Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
    Gene: HDA2, PLO2, YDR295C
    Database cross-references and differences (RAF-indexed):
  • Heterogens: ZN

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records:
    >6z6pA (A:)
    phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqease
    aylvalfedtnlcaihakrvtimpkdiqlarrirger
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records:
    >6z6pB (B:)
    kvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrk
    tvtamdvvyalkrqgrtlygfgg
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >6z6pC (C:)
    trssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardnkk
    triiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >6z6pD (D:)
    ktrkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstit
    sreiqtavrlllpgelakhavsegtkavtkytsak
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >6z6pE (E:)
    hryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeasea
    ylvalfedtnlcaihakrvtimpkdiqlarrirgera
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >6z6pF (F:)
    niqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktvtam
    dvvyalkrqgrtlygfgg
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records:
    >6z6pG (G:)
    aktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardn
    kktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records:
    >6z6pH (H:)
    trkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstits
    reiqtavrlllpgelakhavsegtkavtkytsa
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6z6pK (K:)
    rqvivpvcmpkihysplktglcydvrmryhakiftsyfeyidphpedprriyriykilae
    nglindptlsgvddlgdlmlkipvraatseeilevhtkehlefiestekmsreellkete
    kgdsvyfnndsyasarlpcggaieackavvegrvknslavvrppghhaepqaaggfclfs
    nvavaaknilknypesvrrimildwdihhgngtqksfyqddqvlyvslhrfemgkyypgt
    iqgqydqtgegkgegfncnitwpvggvgdaeymwafeqvvmpmgrefkpdlviissgfda
    adgdtigqchvtpscyghmthmlkslargnlcvvleggynldaiarsalsvakvligepp
    delpdplsdpkpeviemidkvirlqskywncfrrrhansgcnfnepindsiisknfplqk
    airqqqqhylsdefnfvtlplvsmdlpdntvlctpnisesntiiivvhdtsdiwakrnvi
    sgtidlsssviidnsldfikwgldrkygiidvnipltlfepdnysgmitsqevliylwdn
    yikyfpsvakiafigigdsysgivhllghrdtravtktvinflgdkqlkplvplvdetls
    ewyfknslifsnnshqcwkenesrkprkkfgrvlrcdtdglnniieerfeeatdfildsf
    e
    

    Sequence, based on observed residues (ATOM records):
    >6z6pK (K:)
    rqvivpvcmpkihysplktglcydvrmryhakiftsyfeyidphpedprriyriykilae
    nglindptlsgvddlgdlmlkipvraatseeilevhtkehlefiestekmsreellkete
    kgdsvyfnndsyasarlpcggaieackavvegrvknslavvrppghhaepqaaggfclfs
    nvavaaknilknypesvrrimildwdihhgngtqksfyqddqvlyvslhrfemgkyypgt
    iqgqydqtgegkgegfncnitwpvggvgdaeymwafeqvvmpmgrefkpdlviissgfda
    adgdtigqchvtpscyghmthmlkslargnlcvvleggynldaiarsalsvakvligepp
    delpdplsdpkpeviemidkvirlqskywncfrrrhansgpindsiisknfplqkairqq
    qqhylsdefnfvtlplvsmdlpdntvlctpnisesntiiivvhdtsdiwakrnvisgtid
    lsssviidnsldfikwgldrkygiidvnipltlfepdnysgmitsqevliylwdnyikyf
    psvakiafigigdsysgivhllghrdtravtktvinflgdkqlkplvplvdetlsewyfk
    nslifsnnshqcwkkprkkfgrvlrcdtdglnniieerfeeatdfildsfe
    

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6z6pL (L:)
    enslsttskskrqvivpvcmpkihysplktglcydvrmryhakiftsyfeyidphpedpr
    riyriykilaenglindptlsgvddlgdlmlkipvraatseeilevhtkehlefiestek
    msreellketekgdsvyfnndsyasarlpcggaieackavvegrvknslavvrppghhae
    pqaaggfclfsnvavaaknilknypesvrrimildwdihhgngtqksfyqddqvlyvslh
    rfemgkyypgtiqgqydqtgegkgegfncnitwpvggvgdaeymwafeqvvmpmgrefkp
    dlviissgfdaadgdtigqchvtpscyghmthmlkslargnlcvvleggynldaiarsal
    svakvligeppdelpdplsdpkpeviemidkvirlqskywncfrrrhansgcnfnepind
    siisknfplqkairqqqqhylsdefnfvtlplvsmdlpdntvlctpnisesntiiivvhd
    tsdiwakrnvisgtidlsssviidnsldfikwgldrkygiidvnipltlfepdnysgmit
    sqevliylwdnyikyfpsvakiafigigdsysgivhllghrdtravtktvinflgdkqlk
    plvplvdetlsewyfknslifsnnshqcwkenesrkprkkfgrvlrcdtdglnniieerf
    eeatdfildsfe
    

    Sequence, based on observed residues (ATOM records):
    >6z6pL (L:)
    enslsttskskrqvivpvcmpkihysplktglcydvrmryhakiftsyfeyidphpedpr
    riyriykilaenglindptlsgvddlgdlmlkipvraatseeilevhtkehlefiestek
    msreellketekgdsvyfnndsyasarlpcggaieackavvegrvknslavvrppghhae
    pqaaggfclfsnvavaaknilknypesvrrimildwdihhgngtqksfyqddqvlyvslh
    rfemgkyypgtiqgqydqtgegkgegfncnitwpvggvgdaeymwafeqvvmpmgrefkp
    dlviissgfdaadgdtigqchvtpscyghmthmlkslargnlcvvleggynldaiarsal
    svakvligeppdelpdplsdpkpeviemidkvirlqskywncfrrrhansgcnfnepind
    siisknfplqkairqqqqhylsdefnfvtlplvsmdlpdntvlctpnisesntiiivvhd
    tsdiwakrnvisgtidlsssviidnsldfikwgldrkygiidvnipltlfepdnysgmit
    sqevliylwdnyikyfpsvakiafigigdsysgivhllghrdtravtktvinflgdkqlk
    plvplvdetlsewyfknslifsnnshqckkfgrvlrcdtdlnniieerfeeatdfildsf
    e
    

  • Chain 'M':
    Sequence, based on SEQRES records:
    >6z6pM (M:)
    sgdywlpttmslyqkeltdqivslhysdilryfetshykedvilesmktmclngslvath
    pyllidhympkslitrdvpahlaensgkfsvlrdlinlvqeyetetaivcrpgrtmdlle
    alllgnkvhikrydghsikskqkandfsctvhlfsseginftkypikskarfdmlicldt
    tvdtsqkdiqyllqykrerkgleryapivrlvainsidhcrlffgkkfdknsreylenvt
    aamvilrdrlgtlppdlrpiysqklhylvewlenptvpwplpdiyplkqytsmdversll
    tevhfkknssnvnyhlssgiithkliqsmgevymdicvqkqelddysclddlqndhlkff
    snedekiikeyetvlrtnnenlnrshelevennlkfsqietlekdietlkgslmaqgetl
    sklkdafvktdnvqdeiekeervsvsrdtekkymeqeikravdaireneeethklnekqn
    gleselklkfekseistkelnekigflkkelklendlneelvgqlsktmdnlenltiprv
    rtq
    

    Sequence, based on observed residues (ATOM records):
    >6z6pM (M:)
    sgdywlpttmslyqkeltdqivslhysdilryfetshykedvilesmktmclngslvath
    pyllidhympkslitrdvpahlaensgkfsvlrdlinlvqeyetetaivcrpgrtmdlle
    alllgnkvhikrydghsikskndfsctvhlfsseginftkypikskarfdmlicldttvd
    tsqkdiqyllqykrryapivrlvainsidhcrlffgkkfdknsreylenvtaamvilrdr
    lgtlppdlrpiysqklhylvewlenptvpwplpdiyplkqytsmdverslltevhfkkns
    snvnyhlssgiithkliqsmgevymdicvqkqelddysclddlqndhlkffsnedekiik
    eyetvlrtnnenlnrshelevennlkfsqietlekdietlkgslmaqgetlsklkdafvk
    tdnvqdeiekeervsvsrdtekkymeqeikravdaireneeethklnekqngleselklk
    fekseistkelnekigflkkelklendlneelvgqlsktmdnlenltiprvrtq
    

  • Chain 'N':
    Sequence, based on SEQRES records:
    >6z6pN (N:)
    kvyylpvtltqfqkdlseilislhaksfkasiigepqadavnkpsglpagpethpyptls
    qrqltyifdsniraianhpsllvdhymprqllrmeptessiagshkfqvlnqlinsicfr
    dregspnevikcaiiahsikeldlleglilgkkfrtkrlsgtslynekhkfpnlptvdst
    inkdgtpnsvsstssnsnstsytgyskddydysvkrnlkkrkintddwlflattkhlkhd
    qyllanydidmiisfdpmlevelpalqvlrnnankdipiikllvqnspdhylldseikns
    svksshlsnnghvddsqeyeeikssllyflqarnapvnnceidyiklvkcclegkdcnni
    lpvldlitldeaskdssdsgfwqpqltklqysstelplwdgpldiktyqtelmhravirl
    rdiqdeyakgtvplyekrlnetqrqnqldeiknsvgltfkkkqeveksindsekrlkham
    testklqnkinhllknrqelenfnklpsntissenhleegsaladklkeyidknatlfnk
    lkelqqanaeksklndelrskyqiesskaaesaqtlkilqesmkslenevngpltkfste
    slkkelerlqndfqslkarnkflknyitl
    

    Sequence, based on observed residues (ATOM records):
    >6z6pN (N:)
    kvyylpvtltqfqkdlseilislhaksfkasiiptlsqrqltyifdsniraianhpsllv
    dhymprqllrmeptessiagshkfqvlnqlinsicfrdrpnevikcaiiahsikeldlle
    glilgkkfrtkrlsgtslynekhkfpnytgyskddydysvkrnlkkrkintddwlflatt
    khlkhdqyllanydidmiisfdpmlevelpalqvlrnnankdipiikllvqnspdhylld
    seiknsqeyeeikssllyflqarnapvnnceidyiklvkcclegkdcnnilpvldlitsg
    fwqpqltklqysstelplwdgpldiktyqtelmhravirlrdiqdeyakgtvplyekrln
    etqrqnqldeiknsvgltfkkkqeveksindsekrlkhamtestklqnkinhllknrqel
    enfnklpsntissenhleegsaladklkeyidknatlfnklkelqqanaeksklndelrs
    kyqiesskaaesaqtlkilqesmkslenevngpltkfstesqndfqslkarnkflknyit
    l