Structure of PDB 4w2i Chain DG

Receptor sequence

>4w2iDG (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

3D structure

• PDB: 4w2i Negamycin Interferes with Decoding and Translocation by Simultaneous Interaction with rRNA and tRNA.
• Chain: DG
• Resolution: 2.7 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	K36 V38 N40 G42 L43 E45 T71 A73 K75 N79 F80 I88 R91 S124 D126 R128 N132 L135 G154 M155 D156 A158	K35 V37 N39 G41 L42 E44 T70 A72 K74 N78 F79 I87 R90 S123 D125 R127 N131 L134 G153 M154 D155 A157
BS03	rna	DG	P2 N27 W29 E30 Q66 K67 A69 V70 R72 R91 V92 T93 R95 R96 R98	P1 N26 W28 E29 Q65 K66 A68 V69 R71 R90 V91 T92 R94 R95 R97
BS04	MG	DG	R128 G129 N130 T161 A163	R127 G128 N129 T160 A162

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:4w2i, PDBe:4w2i, PDBj:4w2i
• PDBsum: 4w2i
• PubMed: 25306922
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)