Structure of PDB 6p1h Chain A Binding Site BS03

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 IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain6p1h Chain A Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6p1h Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		C1056 C1059 C1069 N1071 C1074 R1080
Binding residue
(residue number reindexed from 1)		C918 C921 C931 N933 C936 R942
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:6p1h, PDBe:6p1h, PDBj:6p1h
PDBsum6p1h
PubMed31582849
UniProtP15436|DPOD_YEAST DNA polymerase delta catalytic subunit (Gene Name=POL3)

[Back to BioLiP]