Structure of PDB 5j4d Chain RC

Receptor sequence

>5j4dRC (length=208) Species: 262724 (Thermus thermophilus HB27)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 5j4d Structural Basis for Translation Termination on a Pseudouridylated Stop Codon.
• Chain: RC
• Resolution: 3.1 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	RC	G2 R3 P7 V8 R10 R13 R14 K22 G23 E24 R25 K30 R35 R36 Y38 P40 G41 Q42 H43 K46 R49 Y54 A55 R59 Q62 R66 E72 R73 Q74 K84 S113 R115 Q116 R118 Q119 R122 H123 H125 R132 D134 L135 P136 S137 Y138 R141 L155 S208 R209	G1 R2 P6 V7 R9 R12 R13 K21 G22 E23 R24 K29 R34 R35 Y37 P39 G40 Q41 H42 K45 R48 Y53 A54 R58 Q61 R65 E71 R72 Q73 K83 S112 R114 Q115 R117 Q118 R121 H122 H124 R131 D133 L134 P135 S136 Y137 R140 L154 S207 R208
BS02	MG	RC	G87 T89	G86 T88
BS03	MG	RC	K85 K86	K84 K85
BS04	MG	RC	Y20 Y27	Y19 Y26
BS05	MG	RC	P51 S52	P50 S51

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5j4d, PDBe:5j4d, PDBj:5j4d
• PDBsum: 5j4d
• PubMed: 27107638
• UniProt: P62664|RS4_THET2 Small ribosomal subunit protein uS4 (Gene Name=rpsD)