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6MYZ

Crystal structure of Tdp1 catalytic domain in complex with compound XZ520

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 K7D A 701
ChainResidue
ATYR204
AHOH883
AHOH909
AHIS263
ALYS265
AASN283
AGLY458
AHIS493
ALYS495
ATRP590
AHOH801

site_idAC2
Number of Residues7
Detailsbinding site for residue EDO A 702
ChainResidue
AILE355
AGLY356
ASER357
ATHR513
AALA515
ATRP522
AGLY540

site_idAC3
Number of Residues4
Detailsbinding site for residue EDO A 703
ChainResidue
AASP322
AASN369
ATRP370
AHOH989

site_idAC4
Number of Residues5
Detailsbinding site for residue EDO A 704
ChainResidue
AILE305
ALYS311
ASER312
ALYS320
AHIS343

site_idAC5
Number of Residues7
Detailsbinding site for residue EDO B 701
ChainResidue
BILE355
BGLY356
BSER357
BTHR513
BALA515
BTRP522
BGLY540

site_idAC6
Number of Residues4
Detailsbinding site for residue EDO B 702
ChainResidue
BGLY229
BASP230
BLYS231
BARG232

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Nucleophile => ECO:0000269|PubMed:12470949, ECO:0000269|PubMed:15111055
ChainResidueDetails
AHIS263
BHIS263

site_idSWS_FT_FI2
Number of Residues2
DetailsACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:12470949, ECO:0000269|PubMed:15111055
ChainResidueDetails
AHIS493
BHIS493

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:12470949
ChainResidueDetails
ALYS265
ALYS495
BLYS265
BLYS495

site_idSWS_FT_FI4
Number of Residues2
DetailsSITE: Interaction with DNA => ECO:0000269|PubMed:12470949
ChainResidueDetails
ASER518
BSER518

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332
ChainResidueDetails
ASER148
BSER148

220113

PDB entries from 2024-05-22

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