Structure of PDB 9b00 Chain 2d

Receptor sequence

>9b002d (length=208) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

PDB

9b00 Berberine analog of chloramphenicol exhibits a distinct mode of action and unveils ribosome plasticity.

Chain

Resolution

2.8 Å

3D
structure

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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)
BS01	rna	2d	G2 R3 I5 P7 V8 C9 R10 R13 R14 K22 G23 R25 K30 R35 R36 Y38 P40 G41 Q42 H43 Q45 K46 S52 L58 R59 K61 Q62 R65 S71 E72 R73 N77 K86 S113 R115 Q116 R118 Q119 H123 H125 R132 V133 D134 L135 S137 L155 L157 E205 R209	G1 R2 I4 P6 V7 C8 R9 R12 R13 K21 G22 R24 K29 R34 R35 Y37 P39 G40 Q41 H42 Q44 K45 S51 L57 R58 K60 Q61 R64 S70 E71 R72 N76 K85 S112 R114 Q115 R117 Q118 H122 H124 R131 V132 D133 L134 S136 L154 L156 E204 R208
BS02	MG	2d	K85 G87	K84 G86
BS03	SF4	2d	C9 C12 K18 L19 K22 R25 C26 C31 M33	C8 C11 K17 L18 K21 R24 C25 C30 M32

External links

PDB	RCSB:9b00, PDBe:9b00, PDBj:9b00
PDBsum	9b00
PubMed	39019034
UniProt	P80373\|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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