Structure of PDB 6xqd Chain 1S

Receptor sequence

>6xqd1S (length=110) Species: 300852 (Thermus thermophilus HB8)

RLTAYERRKFRVRNRIKRTGRLRLSVFRSLKHIYAQIIDDEKGVTLVSAS
SLALKLKGNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKALA
EGAREGGLEF

3D structure

• PDB: 6xqd Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome.
• Chain: 1S
• Resolution: 2.8 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	1S	R3 L4 A6 R9 R10 F12 R13 N16 R17 I18 T21 R23 F87 R89 Y94 R106 F112	R1 L2 A4 R7 R8 F10 R11 N14 R15 I16 T19 R21 F85 R87 Y92 R104 F110
BS02	rna	1S	R15 R25 F29 R30 S31 L32 K33 Y36 Q38 G45 V46 T47 S50 L54 N61 K62 T63 Y92 K93 H95 G96 R97	R13 R23 F27 R28 S29 L30 K31 Y34 Q36 G43 V44 T45 S48 L52 N59 K60 T61 Y90 K91 H93 G94 R95
BS03	MG	1S	K62 R97	K60 R95

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xqd, PDBe:6xqd, PDBj:6xqd
• PDBsum: 6xqd
• PubMed: 32817463
• UniProt: Q5SHQ4|RL18_THET8 Large ribosomal subunit protein uL18 (Gene Name=rplR)