Structure of PDB 6ndk Chain RQ

Receptor sequence

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

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

3D structure

• PDB: 6ndk Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing intRNACGGProfor decoding
• Chain: RQ
• Resolution: 3.64 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	RQ	R5 R6 K8 Y9 K11 Q13 R14 G15 R16 K18 K22 G24 Y26 A28 F29 Q45 Q46 A49 R56 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 R101 H123 K124 L125 P126 K128	R5 R6 K8 Y9 K11 Q13 R14 G15 R16 K18 K22 G24 Y26 A28 F29 Q45 Q46 A49 R56 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 R101 H123 K124 L125 P126 K128
BS02	rna	RQ	R16 L17 G19	R16 L17 G19
BS03	MG	RQ	L125 I127	L125 I127

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:6ndk, PDBe:6ndk, PDBj:6ndk
• PDBsum: 6ndk
• PubMed: 30782843
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)