Structure of PDB 6oxa Chain QD

Receptor sequence

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

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 6oxa Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
• Chain: QD
• Resolution: 3.25 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	QD	G2 R3 Y4 I5 P7 V8 C9 R10 R13 R14 K22 E24 R25 K30 R35 R36 Y38 G41 Q42 H43 R49 Y54 R59 K61 Q62 R66 E72 R73 Q74 G87 S113 R115 Q116 R118 Q119 R122 H123 H125 R131 R132 V133 D134 L135 S137 K151 S208 R209	G1 R2 Y3 I4 P6 V7 C8 R9 R12 R13 K21 E23 R24 K29 R34 R35 Y37 G40 Q41 H42 R48 Y53 R58 K60 Q61 R65 E71 R72 Q73 G86 S112 R114 Q115 R117 Q118 R121 H122 H124 R130 R131 V132 D133 L134 S136 K150 S207 R208
BS02	SF4	QD	C9 C12 L21 K22 R25 C26 C31	C8 C11 L20 K21 R24 C25 C30
BS03	MG	QD	V121 G124 H125 I126 V133	V120 G123 H124 I125 V132

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:6oxa, PDBe:6oxa, PDBj:6oxa
• PDBsum: 6oxa
• PubMed: 31501867
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)