Structure of PDB 8ud6 Chain 2d

Receptor sequence

>8ud62d (length=208) Species: 300852 (Thermus thermophilus HB8)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 8ud6 An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance
• Chain: 2d
• Resolution: 2.7 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	2d	G2 R3 I5 P7 V8 C9 R10 R13 R14 K22 G23 E24 R25 K30 R35 R36 Y38 P40 G41 Q42 H43 Q45 K46 S52 Y54 L58 R59 Q62 R66 E72 R73 K86 S113 R115 Q116 R118 Q119 R122 H123 H125 V133 D134 L135 S137 Y138 L155 E205 S208 R209	G1 R2 I4 P6 V7 C8 R9 R12 R13 K21 G22 E23 R24 K29 R34 R35 Y37 P39 G40 Q41 H42 Q44 K45 S51 Y53 L57 R58 Q61 R65 E71 R72 K85 S112 R114 Q115 R117 Q118 R121 H122 H124 V132 D133 L134 S136 Y137 L154 E204 S207 R208
BS02	MG	2d	A82 S83 K85 T89	A81 S82 K84 T88
BS03	SF4	2d	C9 C12 L19 K22 C26 C31 M33	C8 C11 L18 K21 C25 C30 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:8ud6, PDBe:8ud6, PDBj:8ud6
• PDBsum: 8ud6
• PubMed: 38359125
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)