Structure of PDB 2pup Chain B Binding Site BS02

Receptor Information
>2pup Chain B (length=370) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YETLNESSAVALAVKLGLTLTCQEIGDNYVFHIYDQERALIIKQAVPWPL
TIDRARIESSALIRQGEHVPHLVPRVFYSDTEMAVTVMEDLSHLKIARKG
LIEGENYPHLSQHIGEFLGKTLFYSSDYALEPKVKKQLVKQFTNPELCDI
TERLVFTDPFFDHDTNDFEEELRPFVEKLWNNDSVKIEAAKLKKSFLTSA
ETLIHGDLHTGSIFASEHETKVIDPEFAFYGPIGFDVGQFIANLFLNALS
RDGADREPLYEHVNQVWETFEETFSEAWQKDSLDVYANIDGYLTDTLSHI
FEEAIGFAGCELIRRTIGLAHVADLDTIVPFDKRIGRKRLALETGTAFIE
KRSEFKTITDVIELFKLLVK
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 chain2pup Chain B Residue 999 [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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PDB2pup Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding
Resolution2.6 Å
Binding residue
(original residue number in PDB)		N44 V46 I59 K61 M114 D116 L117 F240 D250 E252
Binding residue
(residue number reindexed from 1)		N28 V30 I41 K43 M88 D90 L91 F214 D224 E226
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.100: S-methyl-5-thioribose kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046522 S-methyl-5-thioribose kinase activity
Biological Process
GO:0009086 methionine biosynthetic process
GO:0016310 phosphorylation
GO:0019509 L-methionine salvage from methylthioadenosine

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2pup, PDBe:2pup, PDBj:2pup
PDBsum2pup
PubMed17522047
UniProtO31663|MTNK_BACSU Methylthioribose kinase (Gene Name=mtnK)

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