Structure of PDB 4v7w Chain DG

Receptor sequence

>4v7wDG (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

3D structure

• PDB: 4v7w Revisiting the structures of several antibiotics bound to the bacterial ribosome.
• Chain: DG
• 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	DG	N40 L43 G44 T71 K74 K75 N79 S124 D126 R128 N132 L133 G134 L135 R136 R153 G154 M155 D156	N39 L42 G43 T70 K73 K74 N78 S123 D125 R127 N131 L132 G133 L134 R135 R152 G153 M154 D155
BS02	rna	DG	N27 V28 W29 E30 Q66 K67 A69 V70 T71 R91 V92 T93 R95	N26 V27 W28 E29 Q65 K66 A68 V69 T70 R90 V91 T92 R94

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:4v7w, PDBe:4v7w, PDBj:4v7w
• PDBsum: 4v7w
• PubMed: 20876130
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)