Structure of PDB 4m8o Chain A Binding Site BS03

Receptor Information
>4m8o Chain A (length=1126) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLT
NMHATLVSQEVTTNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDES
RVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSN
QLFEARKLLRPILQDNANNNVQRNIYNVKVDAKHLIEDIREYDVPYHVRV
SIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFAIATTKPPLKFPDS
AVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNEN
DEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIG
FAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIE
LDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLN
PDETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETY
VGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSS
VDKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNR
LQPDSIKAERDCASCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFP
NKNKFSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREA
IVCQRENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAK
KMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQM
ARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSML
NYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKE
EGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGD
TLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYE
GQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVA
IFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITI
PAALQGVSNPVPRVEHPDWLKRKIAT
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 chain4m8o 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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PDB4m8o Structural basis for processive DNA synthesis by yeast DNA polymerase epsilon.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D640 V641 A642 S643 M644 Y645 R781 K785 K824 N828 D877
Binding residue
(residue number reindexed from 1)		D587 V588 A589 S590 M591 Y592 R721 K725 K764 N768 D817
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:4m8o, PDBe:4m8o, PDBj:4m8o
PDBsum4m8o
PubMed24292646
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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