Structure of PDB 6ndk Chain RN

Receptor sequence

>6ndkRN (length=140) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV

3D structure

• PDB: 6ndk Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing intRNACGGProfor decoding
• Chain: RN
• 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	RN	K2 T3 L23 G24 R25 T28 R35 K37 N45 F51 T63 K66 K70 Y72 R74 Y75 S76 Y78 L82 K83 H94 R97 H101 A102 K104 G105 M106 P108 G110 P111 L112 R114 R115 K118 K121	K2 T3 L23 G24 R25 T28 R35 K37 N45 F51 T63 K66 K70 Y72 R74 Y75 S76 Y78 L82 K83 H94 R97 H101 A102 K104 G105 M106 P108 G110 P111 L112 R114 R115 K118 K121
BS02	MG	RN	K29 V140	K29 V140

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• 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: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)