Structure of PDB 8ud7 Chain 2G

Receptor sequence

>8ud72G (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

3D structure

• PDB: 8ud7 An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance
• Chain: 2G
• Resolution: 2.55 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	2G	K36 V38 N40 G42 L43 E45 T71 A73 N79 F80 I88 S124 F125 D126 R128 N132 L135 R136 G154 D156	K35 V37 N39 G41 L42 E44 T70 A72 N78 F79 I87 S123 F124 D125 R127 N131 L134 R135 G153 D155
BS02	rna	2G	P2 N27 W29 Q66 K67 A69 V70 R91 V92 T93 R95 R96 R98	P1 N26 W28 Q65 K66 A68 V69 R90 V91 T92 R94 R95 R97
BS03	rna	2G	S76 I77 S78	S75 I76 S77
BS04	MG	2G	R128 G129 N130 T161 A163	R127 G128 N129 T160 A162

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ud7, PDBe:8ud7, PDBj:8ud7
• PDBsum: 8ud7
• PubMed: 38359125
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)