Structure of PDB 4r8u Chain B Binding Site BS03

Receptor Information
>4r8u Chain B (length=338) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKF
GVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLS
LDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKI
ASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCG
DVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAE
DIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQE
HVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLD
Ligand information
Ligand ID1FZ
InChIInChI=1S/C10H18N3O13P3/c1-5-3-13(10(16)11-9(5)15)8-2-6(14)7(25-8)4-24-27(17,18)12-28(19,20)26-29(21,22)23/h3,6-8,14H,2,4H2,1H3,(H,11,15,16)(H2,21,22,23)(H3,12,17,18,19,20)/t6-,7+,8+/m0/s1
InChIKeyYRKUYVYMPXAOAT-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.370CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H18 N3 O13 P3
Name5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
ChEMBL
DrugBank
ZINCZINC000013455017
PDB chain4r8u Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4r8u Fast native-SAD phasing for routine macromolecular structure determination
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D9 M10 D11 C12 F13 F14 S43 T44 R50 S56 D104 K158
Binding residue
(residue number reindexed from 1)		D7 M8 D9 C10 F11 F12 S41 T42 R48 S54 D102 K156
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:4r8u, PDBe:4r8u, PDBj:4r8u
PDBsum4r8u
PubMed25506719
UniProtQ47155|DPO4_ECOLI DNA polymerase IV (Gene Name=dinB)

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