Structure of PDB 5vp2 Chain 1Q Binding Site BS02

Receptor Information
>5vp2 Chain 1Q (length=141) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ
Ligand information
>5vp2 Chain 1B (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]
PDB5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		R16 L17 G19
Binding residue
(residue number reindexed from 1)		R16 L17 G19
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA 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:5vp2, PDBe:5vp2, PDBj:5vp2
PDBsum5vp2
PubMed28505372
UniProtP60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)

[Back to BioLiP]