Structure of PDB 5tgm Chain l3

Receptor sequence

>5tgml3 (length=386) Species: 4932 (Saccharomyces cerevisiae)

SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKA
GMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRS
LTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARI
KKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEK
TVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVAC
IGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKAL
EEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL

3D structure

• PDB: 5tgm Molecular insights into protein synthesis with proline residues.
• Chain: l3
• Resolution: 3.5 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	l3	S2 H3 R4 K5 E7 P9 R10 H11 G12 H13 L14 G15 L17 P18 R19 K20 R21 R26 R28 K30 M53 T54 T55 R62 G64 S65 A75 Y92 R97 G98 L99 R100 S101 L102 T103 T104 W106 R116 R117 F118 Y119 K120 N121 Y123 K124 K126 K128 A129 F130 T131 K132 Y133 R150 Y154 R159 Q173 K174 K175 A179 E180 T221 K222 G223 H224 G225 F226 G228 H231 R232 K236 R240 K241 T242 H243 R244 R247 K248 A250 C251 I252 G253 A254 W255 H256 P257 A258 H259 V260 W262 S263 R266 A267 Q269 R270 Y272 S274 R275 T276 I278 N279 G309 V312 H313 G315 K325 C327 I328 P329 G330 R332 R334 L342 Y343 K349 S363 K364 F365 G366 K367 K376 M380 L383 K384 K385	S1 H2 R3 K4 E6 P8 R9 H10 G11 H12 L13 G14 L16 P17 R18 K19 R20 R25 R27 K29 M52 T53 T54 R61 G63 S64 A74 Y91 R96 G97 L98 R99 S100 L101 T102 T103 W105 R115 R116 F117 Y118 K119 N120 Y122 K123 K125 K127 A128 F129 T130 K131 Y132 R149 Y153 R158 Q172 K173 K174 A178 E179 T220 K221 G222 H223 G224 F225 G227 H230 R231 K235 R239 K240 T241 H242 R243 R246 K247 A249 C250 I251 G252 A253 W254 H255 P256 A257 H258 V259 W261 S262 R265 A266 Q268 R269 Y271 S273 R274 T275 I277 N278 G308 V311 H312 G314 K324 C326 I327 P328 G329 R331 R333 L341 Y342 K348 S362 K363 F364 G365 K366 K375 M379 L382 K383 K384
BS02	OHX	l3	K30 A31	K29 A30
BS03	OHX	l3	R167 L171	R166 L170
BS04	OHX	l3	K384 K385 D386 L387	K383 K384 D385 L386
BS05	MG	l3	E227 H231	E226 H230

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006414 translational elongation
• GO:1990145 maintenance of translational fidelity

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:5tgm, PDBe:5tgm, PDBj:5tgm
• PDBsum: 5tgm
• PubMed: 27827794
• UniProt: P14126|RL3_YEAST Large ribosomal subunit protein uL3 (Gene Name=RPL3)