Structure of PDB 5dge Chain m0

Receptor sequence

>5dgem0 (length=213) Species: 559292 (Saccharomyces cerevisiae S288C)

ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVH
LVSNELEQLSSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINK
MLLQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYK
FPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLSKKGSLEN
NIREFPEYFAAQA

3D structure

• PDB: 5dge Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
• Chain: m0
• Resolution: 3.45 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	m0	R3 R4 A6 R7 C8 Y9 K13 N14 K15 Y22 E63 A64 A67 K74 R90 H92 F94 R98 N100 M102 M115 R116 G117 A118 W119 R154 Y157 K158 P160 D193 G194 A195 F196 K198	R2 R3 A5 R6 C7 Y8 K12 N13 K14 Y21 E62 A63 A66 K73 R89 H91 F93 R97 N99 M101 M107 R108 G109 A110 W111 R146 Y149 K150 P152 D185 G186 A187 F188 K190
BS02	rna	m0	L57 K202 K203 G204 L206	L56 K194 K195 G196 L198
BS03	OHX	m0	N100 Q113 G117	N99 Q105 G109
BS04	OHX	m0	Y216 A218 A219 Q220	Y208 A210 A211 Q212

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006415 translational termination

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5dge, PDBe:5dge, PDBj:5dge
• PDBsum: 5dge
• UniProt: P41805|RL10_YEAST Large ribosomal subunit protein uL16 (Gene Name=RPL10)