Structure of PDB 5ndv Chain N6

Receptor sequence

>5ndvN6 (length=125) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKGGKL

3D structure

PDB

5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.

Chain

Resolution

3.3 Å

3D
structure

Enzymatic activity

Enzyme Commision number

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	N6	A2 K3 Q4 S5 L6 V8 S9 S10 R12 K14 A15 R16 Y19 V29 L30 S32 R40 K46 R60 G61 S62 K87 K89 V90 N91 H100 S102 K103 R121	A1 K2 Q3 S4 L5 V7 S8 S9 R11 K13 A14 R15 Y18 V28 L29 S31 R39 K45 R59 G60 S61 K86 K88 V89 N90 H99 S101 K102 R120
BS02	rna	N6	R13 R16 K17 F20 P23 S24 S25 R28 R51 R52 V73 Y74 R75 L111 D112 K113 D114 R121	R12 R15 K16 F19 P22 S23 S24 R27 R50 R51 V72 Y73 R74 L110 D111 K112 D113 R120

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003735	structural constituent of ribosome

	Biological Process
GO:0002181	cytoplasmic translation
GO:0006412	translation
GO:0042273	ribosomal large subunit biogenesis

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005840	ribosome
GO:0015934	large ribosomal subunit
GO:0022625	cytosolic large ribosomal subunit
GO:0032991	protein-containing complex
GO:0043232	intracellular non-membrane-bounded organelle
GO:1990904	ribonucleoprotein complex

External links

PDB	RCSB:5ndv, PDBe:5ndv, PDBj:5ndv
PDBsum	5ndv
PubMed	29208708
UniProt	P05743\|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)