Structure of PDB 8y38 Chain C

Receptor sequence

>8y38C (length=274) Species: 1280 (Staphylococcus aureus)

AIKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTV
RHHGGGHKRQYRVIDFKRNKDGINAKVDSIQYDPNRSANIALVVYADGEK
RYIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKG
GQIARSAGASAQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHE
LVNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPIGRPSPMSPWG
KPTLGKKTRRGKKSSDKLIVRGRK

3D structure

• PDB: 8y38 Synthetic macrolides overcoming MLS B K-resistant pathogens.
• Chain: C
• Resolution: 2.58 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	C	K4 K7 P8 T10 N11 G12 R13 R14 N15 F21 K31 K35 K39 K40 A41 G42 R43 N45 Q46 G47 K48 L49 T50 V51 R52 H53 H54 G56 H58 K59 R60 Q61 Y62 R63 K68 Y83 R87 V95 D98 G99 K147 K150 Q153 I154 A155 R156 S157 A158 G159 K170 Y171 R177 S178 E180 R182 L198 H200 E201 N204 V205 G206 K207 A208 G209 R210 S211 W213 R217 P218 T219 V220 R221 G222 S223 V224 N226 N228 D229 H232 G235 E236 G237 R238 A239 P240 I241 G242 R243 P244 P246 M247 P249 W250 T254 L255 G256 K257 K258 T259 R260 R261 K263 K264 S266 K275	K3 K6 P7 T9 N10 G11 R12 R13 N14 F20 K30 K34 K38 K39 A40 G41 R42 N44 Q45 G46 K47 L48 T49 V50 R51 H52 H53 G55 H57 K58 R59 Q60 Y61 R62 K67 Y82 R86 V94 D97 G98 K146 K149 Q152 I153 A154 R155 S156 A157 G158 K169 Y170 R176 S177 E179 R181 L197 H199 E200 N203 V204 G205 K206 A207 G208 R209 S210 W212 R216 P217 T218 V219 R220 G221 S222 V223 N225 N227 D228 H231 G234 E235 G236 R237 A238 P239 I240 G241 R242 P243 P245 M246 P248 W249 T253 L254 G255 K256 K257 T258 R259 R260 K262 K263 S265 K274

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y38, PDBe:8y38, PDBj:8y38
• PDBsum: 8y38
• PubMed: 38992047
• UniProt: P60433|RL2_STAAW Large ribosomal subunit protein uL2 (Gene Name=rplB)