Structure of PDB 6nd5 Chain 2Q

Receptor sequence

>6nd52Q (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

3D structure

• PDB: 6nd5 High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition.
• Chain: 2Q
• 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	2Q	P4 R6 K8 Y9 K11 Q12 Q13 R14 R16 K22 G24 Y26 F29 W41 Q46 A49 R56 R67 F69 D71 Y74 K76 K77 E80 V81 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 P126 K128	P4 R6 K8 Y9 K11 Q12 Q13 R14 R16 K22 G24 Y26 F29 W41 Q46 A49 R56 R67 F69 D71 Y74 K76 K77 E80 V81 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 P126 K128
BS02	rna	2Q	R16 L17 G19	R16 L17 G19
BS03	rna	2Q	R51 R60	R51 R60
BS04	MG	2Q	G122 I127	G122 I127
BS05	MG	2Q	P78 N89	P78 N89
BS06	MG	2Q	K77 G84	K77 G84

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:6nd5, PDBe:6nd5, PDBj:6nd5
• PDBsum: 6nd5
• PubMed: 30733327
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)