Structure of PDB 3dnt Chain B Binding Site BS01

Receptor Information
>3dnt Chain B (length=419) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLVTWMNNQRVGELTKLANGAHTFKYAPEWLASRYARPLSLSLPLQRGNI
TSDAVFNFFDNLLPDSPIVRDRIVKRYHAKSRQPFDLLSEIGRDSVGAVT
LIPEDETVTHPIMAWEKLTEARLEEVLTAYKADIPLGMIREENDFRISVA
GAQEKTALLRIGNDWCIPKGITPTTHIIKLPQSVDNEYYCLLLAKELGLN
VPDAEIIKAGNVRALAVERFDRRWNAERTVLLRLPQEDMCQTFGLPSSVK
YESDGGPGIARIMAFLMGSSEALKDRYDFMKFQVFQWLIGATQGHAKNFS
VFIQAGGSYRLTPFYDIISAFPVLGGTGIHISDLKLAMGLNASKGKKTAI
DKIYPRHFLATAKVLRFPEVQMHEILSDFARMIPAALDNVKTSLPTDFPE
NVVTAVESNVLRLHGRLSR
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain3dnt Chain B Residue 501 [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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PDB3dnt Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB.
Resolution1.66 Å
Binding residue
(original residue number in PDB)		V98 A152 G153 A154 Q155 K157 I179 K181 R235 F236 D237 H311 Y331 D332
Binding residue
(residue number reindexed from 1)		V96 A150 G151 A152 Q153 K155 I177 K179 R219 F220 D221 H295 Y315 D316
Annotation score5
Binding affinityMOAD: Kd=18uM
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0000976 transcription cis-regulatory region binding
GO:0001217 DNA-binding transcription repressor activity
GO:0003677 DNA binding
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0043565 sequence-specific DNA binding
GO:0044024 histone H2AS1 kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006355 regulation of DNA-templated transcription
GO:0016310 phosphorylation
GO:0022611 dormancy process
GO:0040008 regulation of growth
GO:0044010 single-species biofilm formation
GO:0045892 negative regulation of DNA-templated transcription
GO:0046677 response to antibiotic
Cellular Component
GO:0005829 cytosol
GO:0032993 protein-DNA complex
GO:0110001 toxin-antitoxin complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dnt, PDBe:3dnt, PDBj:3dnt
PDBsum3dnt
PubMed19150849
UniProtP23874|HIPA_ECOLI Serine/threonine-protein kinase toxin HipA (Gene Name=hipA)

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