Structure of PDB 3adb Chain B Binding Site BS02

Receptor Information
>3adb Chain B (length=247) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNHHHHHMLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESF
PVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSMRRDLINIAKKY
NKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKYKWDE
PFLIIDTTKDIDFNEIAKKLIEKSKEIPKFKNNNISDKIDKETRKIVSEY
IKSKKLDKDKIKEVVELRKEFLKKIKKMEEVDADRVLKEFKDLLNSY
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain3adb Chain B Residue 2002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3adb Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine
Resolution2.8 Å
Binding residue
(original residue number in PDB)		G10 G12 K13 S14 T15 R112 R116
Binding residue
(residue number reindexed from 1)		G17 G19 K20 S21 T22 R119 R123
Annotation score3
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:3adb, PDBe:3adb, PDBj:3adb
PDBsum3adb
PubMed20705242
UniProtQ58933|PSTK_METJA L-seryl-tRNA(Sec) kinase (Gene Name=pstK)

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