Structure of PDB 4w2f Chain DN

Receptor sequence

>4w2fDN (length=140) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV

3D structure

• PDB: 4w2f Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome.
• Chain: DN
• Resolution: 2.4 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	DN	K2 T3 V5 W13 G24 R25 T28 R35 K37 N45 F51 T63 G64 K66 Q69 K70 R74 Y75 S76 Y78 P79 G80 K83 K89 R97 E100 H101 A102 G105 M106 P108 P111 L112 R114 F117 K118 P129 H130 Q133	K2 T3 V5 W13 G24 R25 T28 R35 K37 N45 F51 T63 G64 K66 Q69 K70 R74 Y75 S76 Y78 P79 G80 K83 K89 R97 E100 H101 A102 G105 M106 P108 P111 L112 R114 F117 K118 P129 H130 Q133

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4w2f, PDBe:4w2f, PDBj:4w2f
• PDBsum: 4w2f
• PubMed: 25306919
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)