Structure of PDB 5tkr Chain A Binding Site BS01

Receptor Information
>5tkr Chain A (length=432) Species: 29829 (Lipomyces starkeyi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVLDFTVLGLNSGTSMDGIDCALCHFYQKTPDAPMEFELLEYGEVPLAQP
IKQRVMRMILEDTTSPSELSEVNVILGEHFADAVRQFAAERNVDLSTIDA
IASHGQTIWLLSMPEEGQVKSALTMAEGAILASRTGITSITDFRISDQAA
GRQGAPLIAFFDALLLHHPTKLRACQNIGGIANVCFIPPDVDGRRTDEYY
DFDTGPGNVFIDAVVRHFTNGEQEYDKDGAMGKRGKVDQELVDDFLKMPY
FQLDPPKTTGREVFRDTLAHDLIRRAEAKGLSPDDIVATTTRITAQAIVD
HYRRYAPSQEIDEIFMCGGGAYNPNIVEFIQQSYPNTKIMMLDEAGVPAR
AKEAITFAWQGMEALVGRSIPVPTRVETRQHYVLGKVSPGLNYRSVMKKG
MAFGGDAQQLPWVSEMIVKKKGKVITNNWALE
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5tkr Chain A 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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PDB5tkr Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G22 S24 D26 G188 N217 D221 Y234 D237 G327 G328 Y331
Binding residue
(residue number reindexed from 1)		G13 S15 D17 G179 N208 D212 Y225 D228 G318 G319 Y322
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.232: levoglucosan kinase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0046872 metal ion binding
Biological Process
GO:0006040 amino sugar metabolic process
GO:0009254 peptidoglycan turnover
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5tkr, PDBe:5tkr, PDBj:5tkr
PDBsum5tkr
PubMed28196882
UniProtB3VI55|LGK_LIPST Levoglucosan kinase

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