Structure of PDB 5ndj Chain 65

Receptor sequence

>5ndj65 (length=111) Species: 300852 (Thermus thermophilus HB8)

ARLTAYERRKFRVRNRIKRTGRLRLSVFRSLKHIYAQIIDDEKGVTLVSA
SSLALKLKGNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKAL
AEGAREGGLEF

3D structure

• PDB: 5ndj Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: 65
• Resolution: 3.15 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	65	A2 R3 R9 R10 F12 R13 N16 R17 T21 R23 F87 R89 Y94 E111 F112	A1 R2 R8 R9 F11 R12 N15 R16 T20 R22 F86 R88 Y93 E110 F111
BS02	rna	65	K11 R15 R25 F29 R30 S31 L32 K33 H34 Y36 Q38 G45 V46 T47 S50 K57 K59 N61 K62 T63 Y92 K93 H95 R97	K10 R14 R24 F28 R29 S30 L31 K32 H33 Y35 Q37 G44 V45 T46 S49 K56 K58 N60 K61 T62 Y91 K92 H94 R96

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndj, PDBe:5ndj, PDBj:5ndj
• PDBsum: 5ndj
• PubMed: 29208708
• UniProt: Q5SHQ4|RL18_THET8 Large ribosomal subunit protein uL18 (Gene Name=rplR)