Structure of PDB 5doy Chain 1N

Receptor sequence

>5doy1N (length=140) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV

3D structure

• PDB: 5doy Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.
• Chain: 1N
• Resolution: 2.6 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	1N	K2 T3 W13 T22 G24 R25 T28 R35 K37 N45 F51 T63 K65 K66 Q69 K70 T73 R74 Y75 S76 Y78 P79 G80 L82 K83 K89 H94 R97 E100 H101 A102 G105 M106 P111 L112 R114 K118 H130 Q133	K2 T3 W13 T22 G24 R25 T28 R35 K37 N45 F51 T63 K65 K66 Q69 K70 T73 R74 Y75 S76 Y78 P79 G80 L82 K83 K89 H94 R97 E100 H101 A102 G105 M106 P111 L112 R114 K118 H130 Q133
BS02	MG	1N	V46 M48	V46 M48
BS03	MG	1N	G64 K65 L67	G64 K65 L67
BS04	MG	1N	R25 K29	R25 K29
BS05	MG	1N	L34 R35 M48 G49 L116	L34 R35 M48 G49 L116
BS06	MG	1N	K2 T3 Y4	K2 T3 Y4

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:5doy, PDBe:5doy, PDBj:5doy
• PDBsum: 5doy
• PubMed: 26028538
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)