Structure of PDB 8b6k Chain B Binding Site BS05

Receptor Information
>8b6k Chain B (length=1108) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLT
NMHATLVSQEQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVND
VEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFE
ARKLLRPILQDNANNNVQRNIYNKVDAKHLIEDIREYDVPYHVRVSIDKD
IRVGKWYKVTQQGFIEDTRKIAFADPVVMAFAIATTKPPLKFPDSAVDQI
MMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVAL
LQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDA
EGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPEL
MTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETL
RKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHV
ESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVT
NFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQPDS
IKTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKKKKVLTFDELS
YADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSF
RDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVIL
NSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTD
GIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELK
DPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGS
LAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWL
DVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFL
GEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWT
LDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHP
DWLKRKIA
Ligand information
Ligand IDDCP
InChIInChI=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
InChIKeyRGWHQCVHVJXOKC-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=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 1.5.0C1[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 3.341NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL560403
DrugBankDB03258
ZINCZINC000008215945
PDB chain8b6k Chain B Residue 1202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8b6k A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		V641 S643 Y645 R781 K824 N828 Y831 D877
Binding residue
(residue number reindexed from 1)		V583 S585 Y587 R704 K747 N751 Y754 D800
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
Biological Process
GO:0006260 DNA replication
GO:0006281 DNA repair
Cellular Component
GO:0008622 epsilon DNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8b6k, PDBe:8b6k, PDBj:8b6k
PDBsum8b6k
PubMed37819038
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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