Structure of PDB 6xqe Chain 2G

Receptor sequence

>6xqe2G (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

3D structure

• PDB: 6xqe Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome.
• Chain: 2G
• Resolution: 3.0 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	V38 N40 G42 L43 G44 E45 T71 R72 A73 K75 I77 N79 F80 I88 R91 S124 D126 R128 N132 R136 R153 G154 M155 D156	V37 N39 G41 L42 G43 E44 T70 R71 A72 K74 I76 N78 F79 I87 R90 S123 D125 R127 N131 R135 R152 G153 M154 D155
BS02	rna	2G	P2 N27 W29 E30 Q66 K67 A69 V70 R91 V92 T93 R95 R96	P1 N26 W28 E29 Q65 K66 A68 V69 R90 V91 T92 R94 R95
BS03	rna	2G	S76 I77 S78	S75 I76 S77

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:6xqe, PDBe:6xqe, PDBj:6xqe
• PDBsum: 6xqe
• PubMed: 32817463
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)