Structure of PDB 7kc0 Chain A

Receptor sequence

>7kc0A (length=1004) Species: 4932 (Saccharomyces cerevisiae)

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: A
• Resolution: 3.2 Å

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)	Binding affinity
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

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)