Structure of PDB 2pyw Chain A Binding Site BS03

Receptor Information
>2pyw Chain A (length=417) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FEEFTPLNEKSLVDYIKSTPALSSKIGADKSDDDLVIKEVGDGNLNFVFI
VVGSSGSLVIKQALPYIRCIGESWPMTKERAYFEATTLRKHGNLSPDHVP
EVYHFDRTMALIGMRYLEPPHIILRKGLIAGIEYPFLADHMSDYMAKTLF
FTSLLYHDTTEHRRAVTEFCGNVELCRLTEQVVFSDPYRVSTFNRWTSPY
LDDDAKAVREDSALKLEIAELKSMFCERAQALIHGDLHTGSVMVTQDSTQ
VIDPEFSFYGPMGFDIGAYLGNLILAFFAQDGHATQENDRKEYKQWILRT
IEQTWNLFNKRFIALWDQNKDGPGEAYLADIYNNTEVLKFVQENYMRNLL
HDSLGFGAAKMIRRIVGVAHVEDFESIEEDKRRAICERSALEFAKMLLKE
RRKFKSIGEVVSAIQQQ
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 chain2pyw Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2pyw Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR reveals a more occluded active site than its bacterial homolog
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D44 G45 N48 V50 V61 K63 Y118 L119 I125 M245 D255
Binding residue
(residue number reindexed from 1)		D42 G43 N46 V48 V59 K61 Y116 L117 I123 M243 D253
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:0042802 identical protein binding
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:2pyw, PDBe:2pyw, PDBj:2pyw
PDBsum2pyw
PubMed17961230
UniProtQ9C6D2|MTK_ARATH Methylthioribose kinase (Gene Name=MTK)

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