Structure of PDB 8b79 Chain B Binding Site BS04

Receptor Information
>8b79 Chain B (length=1119) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGW
LTNMHATLVSQQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVN
DVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLF
EARKLLRPILQDNANNNVQRNIYNVVDAKHLIEDIREYDVPYHVRVSIDK
DIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQ
IMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVA
LLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPD
AEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPE
LMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDET
LRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGH
VESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKV
TNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQPD
SIKAERDCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKFSK
KKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQREN
PFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYD
SLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVER
VGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQK
FTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKK
RYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYS
AVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSI
TTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIP
IKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGV
SNPVPRVEHPDWLKRKIAT
Ligand information
Ligand IDUTP
InChIInChI=1S/C9H15N2O15P3/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPGAVKCOVUIYSFO-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H15 N2 O15 P3
NameURIDINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL336296
DrugBankDB04005
ZINCZINC000003861755
PDB chain8b79 Chain B Residue 1201 [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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PDB8b79 A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		D640 V641 S643 G644 Y645 R781 K824 N828 Y831 D877
Binding residue
(residue number reindexed from 1)		D583 V584 S586 G587 Y588 R714 K757 N761 Y764 D810
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:8b79, PDBe:8b79, PDBj:8b79
PDBsum8b79
PubMed37819038
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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