Structure of PDB 8ud8 Chain 1d

Receptor sequence

>8ud81d (length=208) Species: 300852 (Thermus thermophilus HB8)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 8ud8 An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance
• Chain: 1d
• Resolution: 2.6 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	1d	G2 R3 P7 V8 C9 R10 R13 R14 K22 E24 R25 K30 R35 R36 Y38 P40 G41 Q42 H43 R49 S52 Y54 R59 K61 Q62 R65 R66 E72 R73 Q74 S113 R115 Q116 Q119 R122 H123 H125 V133 D134 L135 S137 R141 L155 E205 S208 R209	G1 R2 P6 V7 C8 R9 R12 R13 K21 E23 R24 K29 R34 R35 Y37 P39 G40 Q41 H42 R48 S51 Y53 R58 K60 Q61 R64 R65 E71 R72 Q73 S112 R114 Q115 Q118 R121 H122 H124 V132 D133 L134 S136 R140 L154 E204 S207 R208
BS02	SF4	1d	C9 C12 K18 L19 K22 C26 C31 A32 M33	C8 C11 K17 L18 K21 C25 C30 A31 M32

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:8ud8, PDBe:8ud8, PDBj:8ud8
• PDBsum: 8ud8
• PubMed: 38359125
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)