Structure of PDB 4w2i Chain DG Binding Site BS03

Receptor Information
>4w2i Chain DG (length=181) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK
Ligand information
>4w2i Chain DB (length=120) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ucccccgugcccauagcggcguggaaccacccguucccauuccgaacacg
gaagugaaacgcgccagcgccgaugguacugggcgggcgaccgccuggga
gaguaggucggugcggggga
.<<<<<<<<<<....<<<<<<<<....<<<<<<...............>>
>..>>>...>>>>>>.>><<<.....<.<<<<<<<<....>>>>>>>>..
.>...>>>.>>>>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4w2i Negamycin Interferes with Decoding and Translocation by Simultaneous Interaction with rRNA and tRNA.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		P2 N27 W29 E30 Q66 K67 A69 V70 R72 R91 V92 T93 R95 R96 R98
Binding residue
(residue number reindexed from 1)		P1 N26 W28 E29 Q65 K66 A68 V69 R71 R90 V91 T92 R94 R95 R97
Enzymatic activity
Enzyme Commision number ?
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4w2i, PDBe:4w2i, PDBj:4w2i
PDBsum4w2i
PubMed25306922
UniProtQ5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)

[Back to BioLiP]