Structure of PDB 6dti Chain D

Receptor sequence

>6dtiD (length=208) Species: 300852 (Thermus thermophilus HB8)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 6dti A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.
• Chain: D
• Resolution: 3.54 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 R25 R36 P40 G41 Q42 H43 S52 L58 R59 Q62 R65 E72 R73 Q74 R115 R118 Q119 R122 H123 H125 R132 V133 D134 L135 S137 Y138 L155 E156 S208 R209	G1 R2 I4 P6 V7 C8 R9 R12 R13 K21 R24 R35 P39 G40 Q41 H42 S51 L57 R58 Q61 R64 E71 R72 Q73 R114 R117 Q118 R121 H122 H124 R131 V132 D133 L134 S136 Y137 L154 E155 S207 R208

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:6dti, PDBe:6dti, PDBj:6dti
• PDBsum: 6dti
• PubMed: 31945376
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)