Structure of PDB 4v8d Chain BG

Receptor sequence

>4v8dBG (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

3D structure

• PDB: 4v8d A new understanding of the decoding principle on the ribosome.
• Chain: BG
• 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	BG	S76 S78 R83	S75 S77 R82
BS02	rna	BG	K36 V38 N40 G42 G44 E45 T71 K74 N79 I88 S124 D126 R128 N130 N132 G134 L135 R153 G154 M155 D156 A158	K35 V37 N39 G41 G43 E44 T70 K73 N78 I87 S123 D125 R127 N129 N131 G133 L134 R152 G153 M154 D155 A157
BS03	rna	BG	L3 N27 W29 E30 Q66 K67 A69 V70 T71 V92 T93 R95 R96	L2 N26 W28 E29 Q65 K66 A68 V69 T70 V91 T92 R94 R95

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:4v8d, PDBe:4v8d, PDBj:4v8d
• PDBsum: 4v8d
• PubMed: 22437501
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)