Structure of PDB 5ndw Chain O4

Receptor sequence

>5ndwO4 (length=112) Species: 559292 (Saccharomyces cerevisiae S288C)

AQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSAL
QGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIV
KKVVKEQTEAAK

3D structure

• PDB: 5ndw Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: O4
• Resolution: 3.7 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	O4	A2 R4 V5 F7 R8 R9 R10 N11 P12 Y13 N14 T15 S17 K19 V22 K24 T25 P26 G27 L30 R31 Q33 K36 K37 L38 T40 R41 P42 K43 G45 Q52 G53 I54 S55 T56 R58 P59 R60 Y62 A63 S66 K67 T68 K70 T71 S73 R74 Y76 G77 G78 S79 R80 N83 R88 R91 A92 I95 E96 Q98	A1 R3 V4 F6 R7 R8 R9 N10 P11 Y12 N13 T14 S16 K18 V21 K23 T24 P25 G26 L29 R30 Q32 K35 K36 L37 T39 R40 P41 K42 G44 Q51 G52 I53 S54 T55 R57 P58 R59 Y61 A62 S65 K66 T67 K69 T70 S72 R73 Y75 G76 G77 S78 R79 N82 R87 R90 A91 I94 E95 Q97
BS02	ZN	O4	C44 C81	C43 C80

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P87262|RL34A_YEAST Large ribosomal subunit protein eL34A (Gene Name=RPL34A)