Structure of PDB 5vp2 Chain 1V

Receptor sequence

>5vp21V (length=101) Species: 300852 (Thermus thermophilus HB8)

MFAIVKTGGKQYRVEPGLKLRVEKLDAEPGATVELPVLLLGGEKTVVGTP
VVEGASVVAEVLGHGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIR
G

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 1V
• 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	1V	G8 G9 K10 E23 K24 R66 K69 K74 K76 A77 K78 V79 Q80 Y81 R83 K84 K85 G86 H87 Q89 P90	G8 G9 K10 E23 K24 R66 K69 K74 K76 A77 K78 V79 Q80 Y81 R83 K84 K85 G86 H87 Q89 P90
BS02	MG	1V	K76 A77 V79 Q80 R82	K76 A77 V79 Q80 R82
BS03	MG	1V	K78 V79 Q80	K78 V79 Q80
BS04	MG	1V	K84 K85	K84 K85
BS05	MG	1V	E23 K24 P90	E23 K24 P90
BS06	MG	1V	V72 S73	V72 S73

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: P60492|RL21_THET8 Large ribosomal subunit protein bL21 (Gene Name=rplU)