Structure of PDB 5ndg Chain s4

Receptor sequence

>5ndgs4 (length=260) Species: 4932 (Saccharomyces cerevisiae)

ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNR
LKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRL
VYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPD
PNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERH
DGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEE
RDRRRAQQGL

3D structure

• PDB: 5ndg Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Chain: s4
• 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	s4	A2 R3 G4 P5 K6 K7 H8 K10 R11 L12 L19 D21 K22 S24 G25 Y27 A28 P29 R30 A33 G34 K37 L38 R49 N57 G58 R59 A63 M66 K75 R77 K106 R108 Q130 L131 G132 K133 K134 G144 R145 T146 R148 K155 G186 R187 E199 H201 D202 G203 V219 T220 R221 I248 R255	A1 R2 G3 P4 K5 K6 H7 K9 R10 L11 L18 D20 K21 S23 G24 Y26 A27 P28 R29 A32 G33 K36 L37 R48 N56 G57 R58 A62 M65 K74 R76 K105 R107 Q129 L130 G131 K132 K133 G143 R144 T145 R147 K154 G185 R186 E198 H200 D201 G202 V218 T219 R220 I247 R254

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:0032991 protein-containing complex
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: P0CX35|RS4A_YEAST Small ribosomal subunit protein eS4A (Gene Name=RPS4A)