Structure of PDB 6p1h Chain A Binding Site BS05

Receptor Information
>6p1h Chain A (length=959) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKDENTSTVVRFFGVT
SEGHSVLCNVTGFKNYLYVPAPNSSDANDQEQINKFVHYLNETFDHAIDS
IEVVSKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNSWFS
NGTTTYDNIAYTLRLMVDCGIVGMSWITLPKGKYSMIEPNNRVSSCQLEV
SINYRNLIAHPAEGDWSHTAPLRIMSFDIECAGRIGVFPEPEYDPVIQIA
NVVSIAGAKKPFIRNVFTLNTCSPITGSMIFSHATEEEMLSNWRNFIIKV
DPDVIIGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEIKESVFSS
KAYGTRETKNVNIDGRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKED
VHYSIISDLQNGDSETRRRLAVYCLKDAYLPLRLMEKLMALVNYTEMARV
TGVPFSYLLARGQQIKVVSQLFRKCLEIDTVIPNMQSQASDDQYEGATVI
EPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDED
YVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFKRDVL
NGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTKTAVQ
EKYCIKNGYKHDAVVVYGDTDSVMVKFGTTDLKEAMDLGTEAAKYVSTLF
KHPINLEFEKAYFPYLLINKKRYAGLFWTNPDKFDKLDQKGLASVRRDSC
SLVSIVMNKVLKKILIERNVDGALAFVRETINDILHNRVDISKLIISKTL
APNYTNPQPHAVLAERMKRREGVGPNVGDRVDYVIIGGNDKLYNRAEDPL
FVLENNIQVDSRYYLTNQLQNPIISIVAPIIGDKQANGMFVRSGELYIKA
LYDVRDLEEKYSRLWTQCQRCAGNLHSEVLCSNKNCDIFYMRVKVKKELQ
EKVEQLSKW
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain6p1h Chain A Residue 1103 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6p1h Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		D608 F609 D764
Binding residue
(residue number reindexed from 1)		D515 F516 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6p1h, PDBe:6p1h, PDBj:6p1h
PDBsum6p1h
PubMed31582849
UniProtP15436|DPOD_YEAST DNA polymerase delta catalytic subunit (Gene Name=POL3)

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