Structure of PDB 7kc0 Chain A

Receptor sequence

>7kc0A (length=1004) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]

LSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKDENTSTVVRFFGVT
SEGHSVLCNVTGFKNYLYVPAPNSSDANDQEQINKFVHYLNETFDHAIDS
IEVVSKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNSWFS
NGTTTYDNIAYTLRLMVDCGIVGMSWITLPKGKYSMIEPNNRVSSCQLEV
SINYRNLIAHPAEGDWSHTAPLRIMSFSISCAGRIGVFPEPEYDPVIQIA
NVVSIAGAKKPFIRNVFTLNTCSPITGSMIFSHATEEEMLSNWRNFIIKV
DPDVIIGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEIKESVFSS
KAYGTRETKNVNIDGRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKED
VHYSIISDLQNGDSETRRRLAVYCLKDAYLPLRLMEKLMALVNYTEMARV
TGVPFSYLLARGQQIKVVSQLFRKCLEIDTVIPNMQSQASDDQYEGATVI
EPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDED
YVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFKRDVL
NGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTKTAVQ
EKYCIKNGYKHDAVVVYGDTDSVMVKFGTTDLKEAMDLGTEAAKYVSTLF
KHPINLEFEKAYFPYLLINKKRYAGLFWTNPDKFDKLDQKGLASVRRDSC
SLVSIVMNKVLKKILIERNVDGALAFVRETINDILHNRVDISKLIISKTL
APNYTNPQPHAVLAERMKRREGVGPNVGDRVDYVIIGGNDKLYNRAEDPL
FVLENNIQVDSRYYLTNQLQNPIISIVAPIIGDKQANGMFVVKSIKINTG
SQKGGLMSFIKKVEACKSCKGPLRKGEGPLCSNCLARSGELYIKALYDVR
DLEEKYSRLWTQCQRCAGNLHSEVLCSNKNCDIFYMRVKVKKELQEKVEQ
LSKW

3D structure

PDB

7kc0 Structure of eukaryotic DNA polymerase delta bound to the PCNA clamp while encircling DNA.

Chain

Resolution

3.2 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)
BS01	dna	A	D762 D764 K833 G834 V838 R839 R840 D841 T892 Y897 T898 N899 Q901 H903 R923	D669 D671 K740 G741 V745 R746 R747 D748 T799 Y804 T805 N806 Q808 H810 R830
BS02	dna	A	F441 S443 K444 R554 G555 Q556 Q557 Q586 Y587 E588 G589 A590 G709 A713 V715 N812 K813 K934 L935 Y936 N964	F348 S350 K351 R461 G462 Q463 Q464 Q493 Y494 E495 G496 A497 G616 A620 V622 N719 K720 K841 L842 Y843 N871
BS03	SF4	A	Q490 K491 C1056 C1059 C1069 N1071 C1074 R1080	Q397 K398 C963 C966 C976 N978 C981 R987
BS04	D3T	A	F609 S611 Y613 R674 K701 N705 D764	F516 S518 Y520 R581 K608 N612 D671
BS05	MG	A	D608 D764	D515 D671
BS06	ZN	A	C1009 C1012	C916 C919

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

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Biological Process

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Cellular Component

External links

PDB	RCSB:7kc0, PDBe:7kc0, PDBj:7kc0
PDBsum	7kc0
PubMed	33203675
UniProt	P15436\|DPOD_YEAST DNA polymerase delta catalytic subunit (Gene Name=POL3)

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