Structure of PDB 5dge Chain M0

Receptor sequence

>5dgeM0 (length=211) Species: 559292 (Saccharomyces cerevisiae S288C)

ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVH
LVSNELEQLSSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINK
MQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFP
GQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLSKKGSLENNI
REFPEYFAAQA

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 P5 A6 R7 K13 N14 K15 P16 Y22 Y34 D35 K39 S61 E63 A64 A67 R88 R90 H92 F94 R98 M115 R116 G117 W119 G120 Y157 K158 P160 D193 G194 A195 K198	R2 R3 P4 A5 R6 K12 N13 K14 P15 Y21 Y33 D34 K38 S60 E62 A63 A66 R87 R89 H91 F93 R97 M105 R106 G107 W109 G110 Y147 K148 P150 D183 G184 A185 K188
BS02	rna	M0	Y11 E56 L57 K203 G204 S205 L206 N209	Y10 E55 L56 K193 G194 S195 L196 N199
BS03	MG	M0	F159 Q163	F149 Q153
BS04	OHX	M0	N100 K101	N99 K100
BS05	OHX	M0	A187 E215 A218 A219 Q220 A221	A177 E205 A208 A209 Q210 A211

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)