Structure of PDB 8b76 Chain B Binding Site BS07

Receptor Information
>8b76 Chain B (length=1121) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVG
WLTNMHATLVSQENQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDES
RVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSN
QLFEARKLLRPILQDNANNNVQRNIYNVDAKHLIEDIREYDVPYHVRVSI
DKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAV
DQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDE
VALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFA
PDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELD
PELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPD
ETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVG
GHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVD
KVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQ
PDSIKAERDCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKF
SKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQR
ENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVL
YDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALV
ERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVH
QKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGI
KKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGC
YSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKST
SITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSAD
IPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQ
GVSNPVPRVEHPDWLKRKIAT
Ligand information
Ligand IDTTP
InChIInChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyNHVNXKFIZYSCEB-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O14 P3
NameTHYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL363559
DrugBankDB02452
ZINCZINC000008215959
PDB chain8b76 Chain B Residue 1304 [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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PDB8b76 A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		Y431 D640 V641 A642 S643 G644 Y645 R781 K824 N828 D877
Binding residue
(residue number reindexed from 1)		Y376 D585 V586 A587 S588 G589 Y590 R716 K759 N763 D812
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:8b76, PDBe:8b76, PDBj:8b76
PDBsum8b76
PubMed37819038
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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