PDB entry 6dvm

View 6dvm on RCSB PDB site
Description: Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-122
Class: hydrolase/hydrolase inhibitor
Keywords: histone deacetylaase, metallohydrolase, hydrolase-hydrolase inhibitor complex
Deposited on 2018-06-24, released 2018-08-29
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-08-29, with a file datestamp of 2018-08-24.
Experiment type: XRAY
Resolution: 1.47 Å
R-factor: N/A
AEROSPACI score: 0.49 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Hdac6 protein
    Species: Danio rerio [TaxId:7955]
    Gene: HDAC6
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6dvma_
  • Chain 'B':
    Compound: Hdac6 protein
    Species: Danio rerio [TaxId:7955]
    Gene: HDAC6
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6dvmb_
  • Chain 'C':
    Compound: Hdac6 protein
    Species: Danio rerio [TaxId:7955]
    Gene: HDAC6
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6dvmc_
  • Chain 'D':
    Compound: Hdac6 protein
    Species: Danio rerio [TaxId:7955]
    Gene: HDAC6
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6dvmd_
  • Heterogens: ZN, K, HBJ, EDO, BTB, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6dvmA (A:)
    snaggsspitglvydqrmmlhhnmwdshhpelpqrisrifsrheelrllsrchriparla
    teeelalchsskhisiikssehmkprdlnrlgdeynsifisnesytcallaagscfnsaq
    ailtgqvrnavaivrppghhaekdtacgfcffntaaltaryaqsitreslrvlivdwdvh
    hgngtqhifeeddsvlyislhryedgaffpnsedanydkvglgkgrgynvnipwnggkmg
    dpeymaafhhlvmpiarefapelvlvsagfdaargdplggfqvtpegyahlthqlmslaa
    grvliileggynltsisesmsmctsmllgdsppsldhltplktsatvsinnvlrahapfw
    sslr
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dvmA (A:)
    itglvydqrmmlhhnmwdshhpelpqrisrifsrheelrllsrchriparlateeelalc
    hsskhisiikssehmkprdlnrlgdeynsifisnesytcallaagscfnsaqailtgqvr
    navaivrppghhaekdtacgfcffntaaltaryaqsitreslrvlivdwdvhhgngtqhi
    feeddsvlyislhryedgaffpnsedanydkvglgkgrgynvnipwnggkmgdpeymaaf
    hhlvmpiarefapelvlvsagfdaargdplggfqvtpegyahlthqlmslaagrvliile
    ggynltsisesmsmctsmllgdsppsldhltplktsatvsinnvlrahapfwsslr
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6dvmB (B:)
    snaggsspitglvydqrmmlhhnmwdshhpelpqrisrifsrheelrllsrchriparla
    teeelalchsskhisiikssehmkprdlnrlgdeynsifisnesytcallaagscfnsaq
    ailtgqvrnavaivrppghhaekdtacgfcffntaaltaryaqsitreslrvlivdwdvh
    hgngtqhifeeddsvlyislhryedgaffpnsedanydkvglgkgrgynvnipwnggkmg
    dpeymaafhhlvmpiarefapelvlvsagfdaargdplggfqvtpegyahlthqlmslaa
    grvliileggynltsisesmsmctsmllgdsppsldhltplktsatvsinnvlrahapfw
    sslr
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dvmB (B:)
    pitglvydqrmmlhhnmwdshhpelpqrisrifsrheelrllsrchriparlateeelal
    chsskhisiikssehmkprdlnrlgdeynsifisnesytcallaagscfnsaqailtgqv
    rnavaivrppghhaekdtacgfcffntaaltaryaqsitreslrvlivdwdvhhgngtqh
    ifeeddsvlyislhryedgaffpnsedanydkvglgkgrgynvnipwnggkmgdpeymaa
    fhhlvmpiarefapelvlvsagfdaargdplggfqvtpegyahlthqlmslaagrvliil
    eggynltsisesmsmctsmllgdsppsldhltplktsatvsinnvlrahapfwsslr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6dvmC (C:)
    snaggsspitglvydqrmmlhhnmwdshhpelpqrisrifsrheelrllsrchriparla
    teeelalchsskhisiikssehmkprdlnrlgdeynsifisnesytcallaagscfnsaq
    ailtgqvrnavaivrppghhaekdtacgfcffntaaltaryaqsitreslrvlivdwdvh
    hgngtqhifeeddsvlyislhryedgaffpnsedanydkvglgkgrgynvnipwnggkmg
    dpeymaafhhlvmpiarefapelvlvsagfdaargdplggfqvtpegyahlthqlmslaa
    grvliileggynltsisesmsmctsmllgdsppsldhltplktsatvsinnvlrahapfw
    sslr
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dvmC (C:)
    pitglvydqrmmlhhnmwdshhpelpqrisrifsrheelrllsrchriparlateeelal
    chsskhisiikssehmkprdlnrlgdeynsifisnesytcallaagscfnsaqailtgqv
    rnavaivrppghhaekdtacgfcffntaaltaryaqsitreslrvlivdwdvhhgngtqh
    ifeeddsvlyislhryedgaffpnsedanydkvglgkgrgynvnipwnggkmgdpeymaa
    fhhlvmpiarefapelvlvsagfdaargdplggfqvtpegyahlthqlmslaagrvliil
    eggynltsisesmsmctsmllgdsppsldhltplktsatvsinnvlrahapfwsslr
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6dvmD (D:)
    snaggsspitglvydqrmmlhhnmwdshhpelpqrisrifsrheelrllsrchriparla
    teeelalchsskhisiikssehmkprdlnrlgdeynsifisnesytcallaagscfnsaq
    ailtgqvrnavaivrppghhaekdtacgfcffntaaltaryaqsitreslrvlivdwdvh
    hgngtqhifeeddsvlyislhryedgaffpnsedanydkvglgkgrgynvnipwnggkmg
    dpeymaafhhlvmpiarefapelvlvsagfdaargdplggfqvtpegyahlthqlmslaa
    grvliileggynltsisesmsmctsmllgdsppsldhltplktsatvsinnvlrahapfw
    sslr
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dvmD (D:)
    pitglvydqrmmlhhnmwdshhpelpqrisrifsrheelrllsrchriparlateeelal
    chsskhisiikssehmkprdlnrlgdeynsifisnesytcallaagscfnsaqailtgqv
    rnavaivrppghhaekdtacgfcffntaaltaryaqsitreslrvlivdwdvhhgngtqh
    ifeeddsvlyislhryedgaffpnsedanydkvglgkgrgynvnipwnggkmgdpeymaa
    fhhlvmpiarefapelvlvsagfdaargdplggfqvtpegyahlthqlmslaagrvliil
    eggynltsisesmsmctsmllgdsppsldhltplktsatvsinnvlrahapfwsslr