Structure of PDB 3adb Chain B Binding Site BS01

Receptor Information

>3adb Chain B (length=247) Species: 243232 (Methanocaldococcus jannaschii DSM 2661)

MNHHHHHMLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESF
PVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSMRRDLINIAKKY
NKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKYKWDE
PFLIIDTTKDIDFNEIAKKLIEKSKEIPKFKNNNISDKIDKETRKIVSEY
IKSKKLDKDKIKEVVELRKEFLKKIKKMEEVDADRVLKEFKDLLNSY

Ligand information

>3adb Chain D (length=92)

ggccgccgccaccggggugguccccgggccggacuucagauccggcgcgc
cccgaguggggcgcgggguucaauuccccgcggcggccgcca

<<<<<<<<<..<<<<<<....>>>>>><<<<<<.......>>>>>><<<<
<<<....>>>>>>><<<<.......>>>>>>>>>>>>>....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3adb Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): W46 E48 E51 K55 Y78 Y79 N80 S81 M82 R84 I120 V124 M128 D133 K137 K138 Y139 K140 W141 D188 D191 R195 S199 I202 I212 V216 R219 K220 K227 K228
• Binding residue (residue number reindexed from 1): W53 E55 E58 K62 Y85 Y86 N87 S88 M89 R91 I127 V131 M135 D140 K144 K145 Y146 K147 W148 D187 D190 R194 S198 I201 I211 V215 R218 K219 K226 K227
• Binding affinity: PDBbind-CN: Kd=39nM

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

External links

• PDB: RCSB:3adb, PDBe:3adb, PDBj:3adb
• PDBsum: 3adb
• PubMed: 20705242
• UniProt: Q58933|PSTK_METJA L-seryl-tRNA(Sec) kinase (Gene Name=pstK)