PDB entry 6dji

View 6dji on RCSB PDB site
Description: Crystal structure of Tdp1 catalytic domain in complex with compound XZ522
Class: hydrolase/hydrolase inhibitor
Keywords: fragment-based drug design, HYDROLASE-HYDROLASE INHIBITOR complex
Deposited on 2018-05-25, 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: 1.75 Å
R-factor: N/A
AEROSPACI score: 0.38 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: tyrosyl-DNA phosphodiesterase 1
    Species: Homo sapiens [TaxId:9606]
    Gene: TDP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6djia1, d6djia2
  • Chain 'B':
    Compound: tyrosyl-DNA phosphodiesterase 1
    Species: Homo sapiens [TaxId:9606]
    Gene: TDP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6djib1, d6djib2
  • Heterogens: GOG, EDO, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download) 
    >6djiA (A:)
npfqfyltrvsgvkpkynsgalhikdilsplfgtlvssaqfnycfdvdwlvkqyppefrk
kpillvhgdkreakahlhaqakpyenislcqakldiafgthhtkmmlllyeeglrvviht
snlihadwhqktqgiwlsplypriadgthksgespthfkadlisylmaynapslkewidv
ihkhdlsetnvyligstpgrfqgsqkdnwghfrlkkllkdhassmpnaeswpvvgqfssv
gslgadeskwlcsefkesmltlgkesssvplyliypsvenvrtslegypaggslpysiqt
aekqnwlhsyfhkwsaetsgrsnamphiktymrpspdfskiawflvtsanlskaawgale
kngtqlmirsyelgvlflpsafgldsfkvkqkffagpmatfpvpydlppelygskdrpwi
wnipyvkapdthgnmwvp

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

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