Structure of PDB 8pfr Chain LG

Receptor sequence

>8pfrLG (length=386) Species: 4932 (Saccharomyces cerevisiae)

SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKA
GMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRS
LTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARI
KKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEK
TVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVAC
IGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKAL
EEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL

3D structure

• PDB: 8pfr Real-space refinement in PHENIX for cryo-EM and crystallography.
• Chain: LG
• Resolution: 2.15 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	LG	S2 H3 K5 Y6 E7 A8 P9 R10 H11 G12 H13 L14 G15 L17 P18 R19 K20 R21 R26 R28 K30 A31 M53 T54 T55 R62 G64 S65 A75 Y92 T95 R97 L99 R100 S101 T104 R116 R117 F118 Y119 K120 N121 Y123 K124 K126 K128 F130 K132 Y133 R150 Y154 R159 Q173 K174 E180 T221 K222 G223 H224 G225 F226 G228 H231 R232 K236 K237 R240 K241 H243 R244 G245 L246 R247 K248 V249 A250 C251 I252 G253 A254 W255 H256 P257 A258 H259 V260 S263 R266 A267 Q269 R270 S274 R275 T276 I278 N279 M308 G309 H313 G315 C327 I328 P329 G330 R332 K333 R334 L342 Y343 R348 S363 K364 F365 K367 M380 L383 K384	S1 H2 K4 Y5 E6 A7 P8 R9 H10 G11 H12 L13 G14 L16 P17 R18 K19 R20 R25 R27 K29 A30 M52 T53 T54 R61 G63 S64 A74 Y91 T94 R96 L98 R99 S100 T103 R115 R116 F117 Y118 K119 N120 Y122 K123 K125 K127 F129 K131 Y132 R149 Y153 R158 Q172 K173 E179 T220 K221 G222 H223 G224 F225 G227 H230 R231 K235 K236 R239 K240 H242 R243 G244 L245 R246 K247 V248 A249 C250 I251 G252 A253 W254 H255 P256 A257 H258 V259 S262 R265 A266 Q268 R269 S273 R274 T275 I277 N278 M307 G308 H312 G314 C326 I327 P328 G329 R331 K332 R333 L341 Y342 R347 S362 K363 F364 K366 M379 L382 K383

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:8pfr, PDBe:8pfr, PDBj:8pfr
• PDBsum: 8pfr
• UniProt: P14126|RL3_YEAST Large ribosomal subunit protein uL3 (Gene Name=RPL3)