Structure of PDB 8b77 Chain A Binding Site BS03

Receptor Information
>8b77 Chain A (length=1110) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLT
NMHATLVSQEQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVND
VEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFE
ARKLLRPILQDNANNNVQRNIYNVKVDAKHLIEDIREYDVPYHVRVSIDK
DIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFAIATTKPPLKFPDSAVDQ
IMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVA
LLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPD
AEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPE
LMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDET
LRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGH
VESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKV
TNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPD
SIKAERDCASCDFKTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPL
SYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKS
FRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVI
LVSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDT
DGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQEL
KDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDG
SLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRW
LDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDF
LGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRW
TLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEH
PDWLKRKIAT
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain8b77 Chain A Residue 1301 [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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PDB8b77 A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		D640 V641 A642 S643 M644 Y645 R781 K824 V828 D877
Binding residue
(residue number reindexed from 1)		D583 V584 A585 S586 M587 Y588 R705 K748 V752 D801
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

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8b77, PDBe:8b77, PDBj:8b77
PDBsum8b77
PubMed37819038
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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