Structure of PDB 6nd5 Chain 1Y

Receptor sequence

>6nd51Y (length=107) Species: 300852 (Thermus thermophilus HB8)

MRVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVR
VSPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCA
KCGGALD

3D structure

• PDB: 6nd5 High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition.
• Chain: 1Y
• Resolution: 2.6 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	1Y	M1 K4 K8 K9 G18 K19 K21 V30 P32 K34 Y35 V45 K46 K47 A48 V49 R50 V51 G58 G59 F60 H68 S70 K71 R73 R84 R86 K87 K95 K101	M1 K4 K8 K9 G18 K19 K21 V30 P32 K34 Y35 V45 K46 K47 A48 V49 R50 V51 G58 G59 F60 H68 S70 K71 R73 R84 R86 K87 K95 K101
BS02	MG	1Y	I38 V39	I38 V39
BS03	ZN	1Y	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:6nd5, PDBe:6nd5, PDBj:6nd5
• PDBsum: 6nd5
• PubMed: 30733327
• UniProt: Q5SHP9|RL24_THET8 Large ribosomal subunit protein uL24 (Gene Name=rplX)