Structure of PDB 8ud6 Chain 1Q

Receptor sequence

>8ud61Q (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

3D structure

• PDB: 8ud6 An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance
• Chain: 1Q
• Resolution: 2.7 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	1Q	P4 R5 R6 K8 Y9 K11 Q13 R14 R16 L17 K22 G24 Y26 F29 A40 W41 Q46 A49 R56 R67 F69 D71 Y74 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 L125 P126 K128	P4 R5 R6 K8 Y9 K11 Q13 R14 R16 L17 K22 G24 Y26 F29 A40 W41 Q46 A49 R56 R67 F69 D71 Y74 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 L125 P126 K128
BS02	rna	1Q	R16 L17 G19	R16 L17 G19
BS03	rna	1Q	R51 R60	R51 R60
BS04	MG	1Q	T75 K76 G88	T75 K76 G88
BS05	MG	1Q	L125 I127	L125 I127
BS06	MG	1Q	T21 V97 K98 R101	T21 V97 K98 R101
BS07	MG	1Q	R14 Y74 T75	R14 Y74 T75

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:8ud6, PDBe:8ud6, PDBj:8ud6
• PDBsum: 8ud6
• PubMed: 38359125
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)