Structure of PDB 5vp2 Chain 2Q

Receptor sequence

>5vp22Q (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 2Q
• Resolution: 2.8 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	2Q	R5 R6 K8 Y9 K11 Q12 Q13 R14 R16 K22 G24 Y26 W41 Q46 A49 R56 R67 F69 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 P126 K128	R5 R6 K8 Y9 K11 Q12 Q13 R14 R16 K22 G24 Y26 W41 Q46 A49 R56 R67 F69 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 P126 K128
BS02	rna	2Q	R16 L17 G19	R16 L17 G19
BS03	rna	2Q	R56 R60	R56 R60
BS04	MG	2Q	G122 L125 I127	G122 L125 I127
BS05	MG	2Q	P78 N89 E91	P78 N89 E91
BS06	MG	2Q	G84 G86	G84 G86

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

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)