Structure of PDB 5uq8 Chain d

Receptor sequence

>5uq8d (length=208) Species: 300852 (Thermus thermophilus HB8)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 5uq8 Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.
• Chain: d
• Resolution: 3.2 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	d	G2 R3 I5 P7 V8 C9 R10 R13 R14 K22 E24 R25 K30 R35 R36 Y38 P40 G41 Q42 H43 S52 Y54 A55 R59 K61 Q62 R65 R66 S71 E72 R73 Q74 N77 S113 R115 Q116 R118 Q119 R122 H123 H125 V133 D134 L135 S137 Y138 R141 S208 R209	G1 R2 I4 P6 V7 C8 R9 R12 R13 K21 E23 R24 K29 R34 R35 Y37 P39 G40 Q41 H42 S51 Y53 A54 R58 K60 Q61 R64 R65 S70 E71 R72 Q73 N76 S112 R114 Q115 R117 Q118 R121 H122 H124 V132 D133 L134 S136 Y137 R140 S207 R208
BS02	SF4	d	C9 C12 L19 Y20 L21 K22 R25 C26 C31 A32	C8 C11 L18 Y19 L20 K21 R24 C25 C30 A31

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:5uq8, PDBe:5uq8, PDBj:5uq8
• PDBsum: 5uq8
• PubMed: 29456023
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)