Structure of PDB 4ir9 Chain F Binding Site BS03

Receptor Information
>4ir9 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 IDXG4
InChIInChI=1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1
InChIKeyDWGAAFQEGIMTIA-KVQBGUIXSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.7.0c1nc2c(n1C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
FormulaC10 H17 N6 O12 P3
Name2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
ChEMBL
DrugBank
ZINCZINC000032016794
PDB chain4ir9 Chain F Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ir9 A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		D8 M9 D10 C11 F12 F13 S42 T43 R49 D103 K157
Binding residue
(residue number reindexed from 1)		D9 M10 D11 C12 F13 F14 S43 T44 R50 D104 K158
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:4ir9, PDBe:4ir9, PDBj:4ir9
PDBsum4ir9
PubMed23525461
UniProtQ47155|DPO4_ECOLI DNA polymerase IV (Gene Name=dinB)

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