Structure of PDB 1vy4 Chain DG

Receptor sequence

>1vy4DG (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

3D structure

• PDB: 1vy4 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
• Chain: DG
• Resolution: 2.6 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	S76 I77 S78	S75 I76 S77
BS02	rna	DG	V38 N40 G42 L43 G44 E45 T71 K75 I77 N79 F80 I88 S124 F125 D126 R128 N132 L133 G134 L135 R136 G154 M155 D156 A158	V37 N39 G41 L42 G43 E44 T70 K74 I76 N78 F79 I87 S123 F124 D125 R127 N131 L132 G133 L134 R135 G153 M154 D155 A157
BS03	rna	DG	P2 N27 V28 W29 E30 Q66 K67 P68 A69 V70 R91 V92 T93 R95 R98	P1 N26 V27 W28 E29 Q65 K66 P67 A68 V69 R90 V91 T92 R94 R97
BS04	MG	DG	N130 T161	N129 T160

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:1vy4, PDBe:1vy4, PDBj:1vy4
• PDBsum: 1vy4
• PubMed: 25132179
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)