Structure of PDB 5yv1 Chain F Binding Site BS05

Receptor Information
>5yv1 Chain F (length=342) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPAR
KFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEP
LSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLA
KIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRT
CGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTM
AEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTT
QEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP
Ligand information
Ligand IDPO4
InChIInChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
InChIKeyNBIIXXVUZAFLBC-UHFFFAOYSA-K
SMILES
SoftwareSMILES
CACTVS 3.341[O-][P]([O-])([O-])=O
ACDLabs 10.04[O-]P([O-])([O-])=O
OpenEye OEToolkits 1.5.0[O-]P(=O)([O-])[O-]
FormulaO4 P
NamePHOSPHATE ION
ChEMBL
DrugBankDB14523
ZINC
PDB chain5yv1 Chain F Residue 903 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yv1 Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Resolution2.09 Å
Binding residue
(original residue number in PDB)		C11 F12 T43
Binding residue
(residue number reindexed from 1)		C12 F13 T44
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008296 3'-5'-DNA exonuclease activity
GO:0046872 metal ion binding
Biological Process
GO:0000731 DNA synthesis involved in DNA repair
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006974 DNA damage response
GO:0009432 SOS response
GO:0042276 error-prone translesion synthesis
GO:0070987 error-free translesion synthesis
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yv1, PDBe:5yv1, PDBj:5yv1
PDBsum5yv1
PubMed29850882
UniProtQ47155|DPO4_ECOLI DNA polymerase IV (Gene Name=dinB)

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