Structure of PDB 7pir Chain a

Receptor sequence

>7pira (length=285) Species: 272634 (Mycoplasmoides pneumoniae M129)

PIKKIISRSNSGIHHSTVIDYKKLLTTNKNKPEKSLLVTLKKHGGRNNQG
KITVRHQGGRNKRKYRIIDFKRTHYDNIEATVKSIEYDPNRSCFVSLITY
ANGAKSYIISPDGIKVGDKILASEHPIDIKPGFSMPLAFIPEGTQVHNIE
LHPKGGGQIARSAGSYARILGQDETGKYVILQLLSGETRKFLKECRATVG
VVSNLDHNLVVIGKAGRNRHRGIRPTVRGSAMNPNDHPHGGGEGRSPVGR
DAPRTPWGKRHMGVKTRNMKKASTNLIIRNRKGEQ

3D structure

• PDB: 7pir Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Chain: a
• Resolution: 12.1 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	a	I7 S8 R9 S10 N11 S12 G13 I14 H15 H16 Y22 N29 K30 N31 P33 E34 K35 S36 V39 T40 K42 K43 H44 G45 G46 R47 N48 N49 Q50 G51 K52 I53 T54 V55 R56 H57 Q58 G60 R61 N62 K63 R64 K65 Y66 R67 K84 Y88 P90 R92 T100 N103 K106 L152 H153 P154 K155 G156 Q159 I160 A161 R162 S163 A164 G165 S166 K178 Y179 L184 L185 E188 R190 F192 L193 E195 N205 L206 H208 V212 G214 K215 A216 G217 N219 R220 H221 R225 P226 T227 V228 R229 S231 A232 M233 N234 N236 D237 P239 E244 G245 R246 P248 V249 G250 R251 D252 P254 P257 W258 R261 H262 M263 G264 V265 K266 T267 R268 N269 K271 K272 S274 N281 R282 K283 Q286	I6 S7 R8 S9 N10 S11 G12 I13 H14 H15 Y21 N28 K29 N30 P32 E33 K34 S35 V38 T39 K41 K42 H43 G44 G45 R46 N47 N48 Q49 G50 K51 I52 T53 V54 R55 H56 Q57 G59 R60 N61 K62 R63 K64 Y65 R66 K83 Y87 P89 R91 T99 N102 K105 L151 H152 P153 K154 G155 Q158 I159 A160 R161 S162 A163 G164 S165 K177 Y178 L183 L184 E187 R189 F191 L192 E194 N204 L205 H207 V211 G213 K214 A215 G216 N218 R219 H220 R224 P225 T226 V227 R228 S230 A231 M232 N233 N235 D236 P238 E243 G244 R245 P247 V248 G249 R250 D251 P253 P256 W257 R260 H261 M262 G263 V264 K265 T266 R267 N268 K270 K271 S273 N280 R281 K282 Q285
BS02	rna	a	E143 G144 R169 E175	E142 G143 R168 E174

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7pir, PDBe:7pir, PDBj:7pir
• PDBsum: 7pir
• PubMed: 36171285
• UniProt: P75577|RL2_MYCPN Large ribosomal subunit protein uL2 (Gene Name=rplB)