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BioLiP

Structure of PDB 7kc0 Chain A Binding Site BS04

Receptor Information
>7kc0 Chain A (length=1004) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKDENTSTVVRFFGVT
SEGHSVLCNVTGFKNYLYVPAPNSSDANDQEQINKFVHYLNETFDHAIDS
IEVVSKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNSWFS
NGTTTYDNIAYTLRLMVDCGIVGMSWITLPKGKYSMIEPNNRVSSCQLEV
SINYRNLIAHPAEGDWSHTAPLRIMSFSISCAGRIGVFPEPEYDPVIQIA
NVVSIAGAKKPFIRNVFTLNTCSPITGSMIFSHATEEEMLSNWRNFIIKV
DPDVIIGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEIKESVFSS
KAYGTRETKNVNIDGRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKED
VHYSIISDLQNGDSETRRRLAVYCLKDAYLPLRLMEKLMALVNYTEMARV
TGVPFSYLLARGQQIKVVSQLFRKCLEIDTVIPNMQSQASDDQYEGATVI
EPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDED
YVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFKRDVL
NGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTKTAVQ
EKYCIKNGYKHDAVVVYGDTDSVMVKFGTTDLKEAMDLGTEAAKYVSTLF
KHPINLEFEKAYFPYLLINKKRYAGLFWTNPDKFDKLDQKGLASVRRDSC
SLVSIVMNKVLKKILIERNVDGALAFVRETINDILHNRVDISKLIISKTL
APNYTNPQPHAVLAERMKRREGVGPNVGDRVDYVIIGGNDKLYNRAEDPL
FVLENNIQVDSRYYLTNQLQNPIISIVAPIIGDKQANGMFVVKSIKINTG
SQKGGLMSFIKKVEACKSCKGPLRKGEGPLCSNCLARSGELYIKALYDVR
DLEEKYSRLWTQCQRCAGNLHSEVLCSNKNCDIFYMRVKVKKELQEKVEQ
LSKW
Ligand information
Ligand IDD3T
InChIInChI=1S/C10H17N2O13P3/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(23-8)5-22-27(18,19)25-28(20,21)24-26(15,16)17/h4,7-8H,2-3,5H2,1H3,(H,18,19)(H,20,21)(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1
InChIKeyURGJWIFLBWJRMF-JGVFFNPUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CCC(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
CACTVS 3.341CC1=CN([C@H]2CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
CACTVS 3.341CC1=CN([CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O13 P3
Name2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL566812
DrugBank
ZINCZINC000013519271
PDB chain7kc0 Chain A Residue 1102 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7kc0 Structure of eukaryotic DNA polymerase delta bound to the PCNA clamp while encircling DNA.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		F609 S611 Y613 R674 K701 N705 D764
Binding residue
(residue number reindexed from 1)		F516 S518 Y520 R581 K608 N612 D671
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0004527 exonuclease activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008296 3'-5'-DNA exonuclease activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0060090 molecular adaptor activity
Biological Process
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006278 RNA-templated DNA biosynthetic process
GO:0006287 base-excision repair, gap-filling
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0043137 DNA replication, removal of RNA primer
GO:0045004 DNA replication proofreading
GO:0045005 DNA-templated DNA replication maintenance of fidelity
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005657 replication fork
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle
GO:0043625 delta DNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7kc0, PDBe:7kc0, PDBj:7kc0
PDBsum7kc0
PubMed33203675
UniProtP15436|DPOD_YEAST DNA polymerase delta catalytic subunit (Gene Name=POL3)

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