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6DHU

Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT0911 from cocktail soak

Functional Information from GO Data
ChainGOidnamespacecontents
A0005634cellular_componentnucleus
A0006281biological_processDNA repair
A0008081molecular_functionphosphoric diester hydrolase activity
B0005634cellular_componentnucleus
B0006281biological_processDNA repair
B0008081molecular_functionphosphoric diester hydrolase activity
Functional Information from PDB Data
site_idAC1
Number of Residues11
Detailsbinding site for residue GHM A 701
ChainResidue
ATYR204
AASN516
AHOH849
AHIS263
ALYS265
AASN283
ASER399
ASER400
APRO461
AHIS493
ALYS495

site_idAC2
Number of Residues6
Detailsbinding site for residue EDO A 702
ChainResidue
AILE355
AGLY356
ASER357
ATHR513
ATRP522
AGLY540

site_idAC3
Number of Residues5
Detailsbinding site for residue EDO A 703
ChainResidue
ASER198
AGLU337
ATRP338
AHOH905
AHOH920

site_idAC4
Number of Residues8
Detailsbinding site for residue EDO A 704
ChainResidue
ATHR484
ALYS556
AGLN557
ATYR574
AASP575
ALEU576
AHOH833
AHOH928

site_idAC5
Number of Residues5
Detailsbinding site for residue EDO A 705
ChainResidue
AILE305
ALYS311
ASER312
ALYS320
AHIS343

site_idAC6
Number of Residues11
Detailsbinding site for residue GHM B 701
ChainResidue
BTYR204
BHIS263
BLYS265
BASN283
BSER399
BSER400
BPRO461
BHIS493
BLYS495
BASN516
BHOH853

site_idAC7
Number of Residues7
Detailsbinding site for residue EDO B 702
ChainResidue
BILE355
BGLY356
BSER357
BTHR513
BALA515
BTRP522
BGLY540

site_idAC8
Number of Residues3
Detailsbinding site for residue EDO B 703
ChainResidue
BASP322
BASN369
BHOH865

site_idAC9
Number of Residues6
Detailsbinding site for residue EDO B 704
ChainResidue
BTHR484
BLYS556
BGLN557
BTYR574
BLEU576
BHOH832

site_idAD1
Number of Residues5
Detailsbinding site for residue EDO B 705
ChainResidue
BLYS311
BSER312
BLYS320
BHIS343
BHOH1013

site_idAD2
Number of Residues5
Detailsbinding site for residue EDO B 706
ChainResidue
BASN471
BHIS474
BARG586
BILE589
BHOH1032

site_idAD3
Number of Residues5
Detailsbinding site for residue EDO B 707
ChainResidue
BGLU468
BLYS469
BGLN470
BASN471
BTRP472

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
DetailsRegion: {"description":"Interaction with DNA","evidences":[{"source":"PubMed","id":"12470949","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2
DetailsActive site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"12470949","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15111055","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsActive site: {"description":"Proton donor/acceptor","evidences":[{"source":"PubMed","id":"12470949","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15111055","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12470949","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues2
DetailsSite: {"description":"Interaction with DNA","evidences":[{"source":"PubMed","id":"12470949","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

238582

PDB entries from 2025-07-09

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