Structure of PDB 4v8x Chain DG

Receptor sequence

>4v8xDG (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

3D structure

• PDB: 4v8x Yoeb-Ribosome Structure: A Canonical Rnase that Requires the Ribosome for its Specific Activity.
• Chain: DG
• Resolution: 3.35 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 S78 R83 K84	S75 S77 R82 K83
BS02	rna	DG	V38 N40 L43 E45 T71 R72 A73 K74 K75 I77 N79 L90 R91 R128 N132 G134 L135 R136 G154 M155 D156	V37 N39 L42 E44 T70 R71 A72 K73 K74 I76 N78 L89 R90 R127 N131 G133 L134 R135 G153 M154 D155
BS03	rna	DG	N27 W29 E30 K67 V70 T71 R91 V92	N26 W28 E29 K66 V69 T70 R90 V91

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:4v8x, PDBe:4v8x, PDBj:4v8x
• PDBsum: 4v8x
• PubMed: 23945936
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)