Structure of PDB 6oxa Chain XD

Receptor sequence

>6oxaXD (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: XD
• 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	XD	G2 R3 I5 P7 V8 C9 R10 R13 R14 K22 E24 R25 K30 R35 R36 Y38 G41 Q42 H43 Y54 R59 K61 Q62 R66 S71 E72 R73 Q74 G87 S113 R115 Q116 R118 Q119 R122 H123 H125 R131 R132 V133 D134 L135 S137 K151 S208	G1 R2 I4 P6 V7 C8 R9 R12 R13 K21 E23 R24 K29 R34 R35 Y37 G40 Q41 H42 Y53 R58 K60 Q61 R65 S70 E71 R72 Q73 G86 S112 R114 Q115 R117 Q118 R121 H122 H124 R130 R131 V132 D133 L134 S136 K150 S207
BS02	SF4	XD	C9 C12 K18 L21 C26 C31	C8 C11 K17 L20 C25 C30

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)