Structure of PDB 8jdm Chain W

Receptor sequence

>8jdmW (length=180) Species: 9606 (Homo sapiens)

SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLII
RKPVTVHSRARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRI
LRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIHKLKADKAR
KKLLADQAEARRSKTKEARKRREERLQAKK

3D structure

• PDB: 8jdm Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
• Chain: W
• Resolution: 2.67 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	W	M3 L4 R5 K8 R9 R16 G18 K19 K20 K21 W23 L24 S37 R38 Q39 Q40 K43 K46 T56 H58 S59 R60 R62 R64 R74 H75 G77 I78 G79 R81 K82 G83 T84 N86 R88 P90 K92 V93 W95 M96 R100 R103 R104 R108 R110 R117 H118 Y120 H121 Y124 L125 K126 K128 K135 R136	M2 L3 R4 K7 R8 R15 G17 K18 K19 K20 W22 L23 S36 R37 Q38 Q39 K42 K45 T55 H57 S58 R59 R61 R63 R73 H74 G76 I77 G78 R80 K81 G82 T83 N85 R87 P89 K91 V92 W94 M95 R99 R102 R103 R107 R109 R116 H117 Y119 H120 Y123 L124 K125 K127 K134 R135
BS02	rna	W	R162 R163 R170 R172 R173 R176	R161 R162 R169 R171 R172 R175

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:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8jdm, PDBe:8jdm, PDBj:8jdm
• PDBsum: 8jdm
• PubMed: 37992713
• UniProt: P84098|RL19_HUMAN Large ribosomal subunit protein eL19 (Gene Name=RPL19)