Structure of PDB 8jdk Chain Y

Receptor sequence

>8jdkY (length=159) Species: 9606 (Homo sapiens)

TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKG
MPHKCYHGKTGRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKS
RDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELL
EPIPYEFMA

3D structure

• PDB: 8jdk Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
• Chain: Y
• Resolution: 2.26 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	Y	T2 N3 T4 K5 G6 K7 R8 R9 G10 R12 Y13 S16 F19 H22 G23 K36 D41 K43 T47 Q49 K50 G51 H54 K55 Y57 H58 G59 K60 T61 T68 Q69 H70 A71 K78 V80 L85 K87 R88 N90 R92 K97 K100 R102 S104 F105 R108 V109 N112 K116 W125 K129 R130 F140 R142	T1 N2 T3 K4 G5 K6 R7 R8 G9 R11 Y12 S15 F18 H21 G22 K35 D40 K42 T46 Q48 K49 G50 H53 K54 Y56 H57 G58 K59 T60 T67 Q68 H69 A70 K77 V79 L84 K86 R87 N89 R91 K96 K99 R101 S103 F104 R107 V108 N111 K115 W124 K128 R129 F139 R141
BS02	rna	Y	P26 A28	P25 A27

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8jdk, PDBe:8jdk, PDBj:8jdk
• PDBsum: 8jdk
• PubMed: 37992713
• UniProt: P46778|RL21_HUMAN Large ribosomal subunit protein eL21 (Gene Name=RPL21)