Structure of PDB 3a4m Chain A Binding Site BS01

Receptor Information
>3a4m Chain A (length=236) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIMLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKE
KYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSMRRDLINIAKKYNKNYA
IIYLKASLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKYKWDEPFLII
DTTKDIDFNEIAKKLIEKSKEIPKFNISDKIDKETRKIVSEYIKSKKLDK
DKIKEVVELRKEFLKKIKKVDADRVLKEFKDLLNSY
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 chain3a4m Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3a4m Structure of a tRNA-dependent kinase essential for selenocysteine decoding
Resolution1.792 Å
Binding residue
(original residue number in PDB)		G14 G16 K17 S18 T19 R116 R120 T154
Binding residue
(residue number reindexed from 1)		G12 G14 K15 S16 T17 R114 R118 T152
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.164: O-phosphoseryl-tRNA(Sec) kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0043915 L-seryl-tRNA(Sec) kinase activity
Biological Process
GO:0001717 conversion of seryl-tRNAsec to selenocys-tRNAsec
GO:0002098 tRNA wobble uridine modification
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3a4m, PDBe:3a4m, PDBj:3a4m
PDBsum3a4m
PubMed19805283
UniProtQ58933|PSTK_METJA L-seryl-tRNA(Sec) kinase (Gene Name=pstK)

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