Structure of PDB 5dm6 Chain S

Receptor sequence
>5dm6S (length=175) Species: 1299 (Deinococcus radiodurans) [Search protein sequence]
MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTG
LFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHT
TGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAG
DIKLPEGCTLAADPELTVVSVLPPR
3D structure
PDB5dm6 Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
ChainS
Resolution2.9 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number ?
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 S R41 V108 H146 L166 T167 R41 V108 H146 L166 T167
BS02 rna S R8 V22 Y24 K26 N29 S31 K67 Q70 R74 H80 D82 R8 V22 Y24 K26 N29 S31 K67 Q70 R74 H80 D82
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008097 5S rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dm6, PDBe:5dm6, PDBj:5dm6
PDBsum5dm6
PubMed26464437
UniProtQ9RX88|RL25_DEIRA Large ribosomal subunit protein bL25 (Gene Name=rplY)

[Back to BioLiP]