PDB entry 6die

View 6die on RCSB PDB site
Description: Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment benzene-1,2,4-tricarboxylic acid from single soak
Class: hydrolase/hydrolase inhibitor
Keywords: fragment-based drug design, hydrolase-hydrolase inhibitor complex
Deposited on 2018-05-23, released 2019-05-29
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-11-13, with a file datestamp of 2019-11-08.
Experiment type: XRAY
Resolution: 1.78 Å
R-factor: N/A
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Tdp1 catalytic domain (residues 149-609)
    Species: Homo sapiens [TaxId:9606]
    Gene: TDP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6diea1, d6diea2
  • Chain 'B':
    Compound: Tdp1 catalytic domain (residues 149-609)
    Species: Homo sapiens [TaxId:9606]
    Gene: TDP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6dieb1, d6dieb2
  • Heterogens: GHM, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6dieA (A:)
    sgegqdiwdmldkgnpfqfyltrvsgvkpkynsgalhikdilsplfgtlvssaqfnycfd
    vdwlvkqyppefrkkpillvhgdkreakahlhaqakpyenislcqakldiafgthhtkmm
    lllyeeglrvvihtsnlihadwhqktqgiwlsplypriadgthksgespthfkadlisyl
    maynapslkewidvihkhdlsetnvyligstpgrfqgsqkdnwghfrlkkllkdhassmp
    naeswpvvgqfssvgslgadeskwlcsefkesmltlgkesktpgkssvplyliypsvenv
    rtslegypaggslpysiqtaekqnwlhsyfhkwsaetsgrsnamphiktymrpspdfski
    awflvtsanlskaawgalekngtqlmirsyelgvlflpsafgldsfkvkqkffagsqepm
    atfpvpydlppelygskdrpwiwnipyvkapdthgnmwvps
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dieA (A:)
    npfqfyltrvsgvkpkynsgalhikdilsplfgtlvssaqfnycfdvdwlvkqyppefrk
    kpillvhgdkreakahlhaqakpyenislcqakldiafgthhtkmmlllyeeglrvviht
    snlihadwhqktqgiwlsplypriadgthksgespthfkadlisylmaynapslkewidv
    ihkhdlsetnvyligstpgrfqgsqkdnwghfrlkkllkdhassmpnaeswpvvgqfssv
    gslgadeskwlcsefkesmltlgkesssvplyliypsvenvrtslegypaggslpysiqt
    aekqnwlhsyfhkwsaetsgrsnamphiktymrpspdfskiawflvtsanlskaawgale
    kngtqlmirsyelgvlflpsafgldsfkvkqkffapmatfpvpydlppelygskdrpwiw
    nipyvkapdthgnmwvp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6dieB (B:)
    sgegqdiwdmldkgnpfqfyltrvsgvkpkynsgalhikdilsplfgtlvssaqfnycfd
    vdwlvkqyppefrkkpillvhgdkreakahlhaqakpyenislcqakldiafgthhtkmm
    lllyeeglrvvihtsnlihadwhqktqgiwlsplypriadgthksgespthfkadlisyl
    maynapslkewidvihkhdlsetnvyligstpgrfqgsqkdnwghfrlkkllkdhassmp
    naeswpvvgqfssvgslgadeskwlcsefkesmltlgkesktpgkssvplyliypsvenv
    rtslegypaggslpysiqtaekqnwlhsyfhkwsaetsgrsnamphiktymrpspdfski
    awflvtsanlskaawgalekngtqlmirsyelgvlflpsafgldsfkvkqkffagsqepm
    atfpvpydlppelygskdrpwiwnipyvkapdthgnmwvps
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dieB (B:)
    npfqfyltrvsgvkpkynsgalhikdilsplfgtlvssaqfnycfdvdwlvkqyppefrk
    kpillvhgdkreakahlhaqakpyenislcqakldiafgthhtkmmlllyeeglrvviht
    snlihadwhqktqgiwlsplypriadgthksgespthfkadlisylmaynapslkewidv
    ihkhdlsetnvyligstpgrfqgsqkdnwghfrlkkllkdhassmpnaeswpvvgqfssv
    gslgadeskwlcsefkesmltlgkesssvplyliypsvenvrtslegypaggslpysiqt
    aekqnwlhsyfhkwsaetsgrsnamphiktymrpspdfskiawflvtsanlskaawgale
    kngtqlmirsyelgvlflpsafgldsfkvkqkffagpmatfpvpydlppelygskdrpwi
    wnipyvkapdthgnmwvps