Structure of PDB 6p1h Chain A Binding Site BS04

Receptor Information

>6p1h Chain A (length=959) Species: 559292 (Saccharomyces cerevisiae S288C)

LSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKDENTSTVVRFFGVT
SEGHSVLCNVTGFKNYLYVPAPNSSDANDQEQINKFVHYLNETFDHAIDS
IEVVSKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNSWFS
NGTTTYDNIAYTLRLMVDCGIVGMSWITLPKGKYSMIEPNNRVSSCQLEV
SINYRNLIAHPAEGDWSHTAPLRIMSFDIECAGRIGVFPEPEYDPVIQIA
NVVSIAGAKKPFIRNVFTLNTCSPITGSMIFSHATEEEMLSNWRNFIIKV
DPDVIIGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEIKESVFSS
KAYGTRETKNVNIDGRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKED
VHYSIISDLQNGDSETRRRLAVYCLKDAYLPLRLMEKLMALVNYTEMARV
TGVPFSYLLARGQQIKVVSQLFRKCLEIDTVIPNMQSQASDDQYEGATVI
EPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDED
YVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFKRDVL
NGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTKTAVQ
EKYCIKNGYKHDAVVVYGDTDSVMVKFGTTDLKEAMDLGTEAAKYVSTLF
KHPINLEFEKAYFPYLLINKKRYAGLFWTNPDKFDKLDQKGLASVRRDSC
SLVSIVMNKVLKKILIERNVDGALAFVRETINDILHNRVDISKLIISKTL
APNYTNPQPHAVLAERMKRREGVGPNVGDRVDYVIIGGNDKLYNRAEDPL
FVLENNIQVDSRYYLTNQLQNPIISIVAPIIGDKQANGMFVRSGELYIKA
LYDVRDLEEKYSRLWTQCQRCAGNLHSEVLCSNKNCDIFYMRVKVKKELQ
EKVEQLSKW

Ligand information

• Ligand ID: DCP
• InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: RGWHQCVHVJXOKC-SHYZEUOFSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
• Formula: C9 H16 N3 O13 P3
• Name: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL560403
• DrugBank: DB03258
• ZINC: ZINC000008215945
• PDB chain: 6p1h Chain A Residue 1102

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6p1h Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): F609 N610 S611 L612 Y613 R674 K701 D764
• Binding residue (residue number reindexed from 1): F516 N517 S518 L519 Y520 R581 K608 D671
• Annotation score: 1

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

External links

• PDB: RCSB:6p1h, PDBe:6p1h, PDBj:6p1h
• PDBsum: 6p1h
• PubMed: 31582849
• UniProt: P15436|DPOD_YEAST DNA polymerase delta catalytic subunit (Gene Name=POL3)