Structure of PDB 8cvm Chain d

Receptor sequence

>8cvmd (length=214) Species: 1747 (Cutibacterium acnes)

ERTVKGVLGTKLGMTQLWDEHNRLVPVTVIQAGPCVVTQVRTPETDGYSA
VQLGYGAVKAKNVTKPEAGHFEKAGVTPRRHLVELRTADASEYTLGQEIA
ADVFSESDFVDVTGTSKGKGTAGVMKRHGFGGLRATHGVHRKHRSPGSIG
GCSTPGKVIKGLRMAGRMGVERVTVQNLQVHSVDAERGIMLVRGAVPGPK
GSLLVVRSAAKKAA

3D structure

• PDB: 8cvm Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism.
• Chain: d
• Resolution: 2.66 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	d	M17 Q19 P29 Q42 R44 T48 D49 Y51 Q55 K62 K64 N65 T67 K68 P69 G72 H73 K76 R83 L85 E87 R89 S119 K120 G121 K122 G123 T124 G126 K129 F133 G134 G135 L136 R137 T139 H140 G141 H143 R144 K145 H146 R147 P149 G150 S151 I152 G153 G154 C155 S156 T157 P158 G159 K160 V161 I162 K163 G164 L165 R166 M167 A168 R170 R175 V176 T177 Q179 N180 V199 P200 G201 P202 K214	M14 Q16 P26 Q39 R41 T45 D46 Y48 Q52 K59 K61 N62 T64 K65 P66 G69 H70 K73 R80 L82 E84 R86 S116 K117 G118 K119 G120 T121 G123 K126 F130 G131 G132 L133 R134 T136 H137 G138 H140 R141 K142 H143 R144 P146 G147 S148 I149 G150 G151 C152 S153 T154 P155 G156 K157 V158 I159 K160 G161 L162 R163 M164 A165 R167 R172 V173 T174 Q176 N177 V196 P197 G198 P199 K211

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8cvm, PDBe:8cvm, PDBj:8cvm
• PDBsum: 8cvm
• PubMed: 36864821
• UniProt: Q6A6M6|RL3_CUTAK Large ribosomal subunit protein uL3 (Gene Name=rplC)