Structure of PDB 6ny6 Chain D

Receptor sequence

>6ny6D (length=208) Species: 300852 (Thermus thermophilus HB8)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 6ny6 Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
• Chain: D
• Resolution: 3.74 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 P7 V8 C9 R10 R13 R14 K22 E24 R25 K30 R35 R36 Y38 G41 Q42 H43 S52 R59 K61 Q62 R66 E72 R73 Q74 K84 K86 S113 R115 Q116 R118 Q119 R122 H123 H125 R132 V133 D134 L135 P136 S137 Y138 R141 K151 L157 S208 R209	G1 R2 P6 V7 C8 R9 R12 R13 K21 E23 R24 K29 R34 R35 Y37 G40 Q41 H42 S51 R58 K60 Q61 R65 E71 R72 Q73 K83 K85 S112 R114 Q115 R117 Q118 R121 H122 H124 R131 V132 D133 L134 P135 S136 Y137 R140 K150 L156 S207 R208
BS02	SF4	D	C9 C12 K18 Y20 L21 K22 C26 C31 A32	C8 C11 K17 Y19 L20 K21 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:6ny6, PDBe:6ny6, PDBj:6ny6
• PDBsum: 6ny6
• PubMed: 31501867
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)