Structure of PDB 6xqd Chain 2Y

Receptor sequence

>6xqd2Y (length=107) Species: 300852 (Thermus thermophilus HB8)

MRVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVR
VSPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCA
KCGGALD

3D structure

• PDB: 6xqd Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome.
• Chain: 2Y
• 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	2Y	M1 R2 K4 H6 K8 K9 S17 G18 K19 K21 V30 P32 Y35 K46 K47 A48 V49 G59 F60 K63 H68 S70 K71 R73 R84 R86 K87 K95 K101	M1 R2 K4 H6 K8 K9 S17 G18 K19 K21 V30 P32 Y35 K46 K47 A48 V49 G59 F60 K63 H68 S70 K71 R73 R84 R86 K87 K95 K101
BS02	ZN	2Y	C76 C79 C99 C102	C76 C79 C99 C102

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xqd, PDBe:6xqd, PDBj:6xqd
• PDBsum: 6xqd
• PubMed: 32817463
• UniProt: Q5SHP9|RL24_THET8 Large ribosomal subunit protein uL24 (Gene Name=rplX)