Structure of PDB 5ndk Chain E5

Receptor sequence

>5ndkE5 (length=84) Species: 300852 (Thermus thermophilus HB8)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPLA

3D structure

• PDB: 5ndk Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: E5
• Resolution: 2.95 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	E5	H3 S9 T10 N12 R14 D15 S16 A18 K19 R20 K24 R25 Y26 E27 Q29 R32 A33 G34 N35 I36 R39 R41 G42 T43 R44 G54 R55 D56 F57 F60 F69 R74 L75 R77	H2 S8 T9 N11 R13 D14 S15 A17 K18 R19 K23 R24 Y25 E26 Q28 R31 A32 G33 N34 I35 R38 R40 G41 T42 R43 G53 R54 D55 F56 F59 F68 R73 L74 R76
BS02	rna	E5	R72 R74 L75	R71 R73 L74
BS03	rna	E5	A2 G6 R11	A1 G5 R10

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5ndk, PDBe:5ndk, PDBj:5ndk
• PDBsum: 5ndk
• PubMed: 29208708
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)