Structure of PDB 5vp2 Chain 1S

Receptor sequence

>5vp21S (length=110) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]

RLTAYERRKFRVRNRIKRTGRLRLSVFRSLKHIYAQIIDDEKGVTLVSAS
SLALKLKGNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKALA
EGAREGGLEF

3D structure

PDB

5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.

Chain

Resolution

2.8 Å

3D
structure

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)
BS01	rna	1S	R3 L4 A6 R9 R10 F12 R13 N16 R17 I18 T21 R23 F87 R89 Y94 R106 F112	R1 L2 A4 R7 R8 F10 R11 N14 R15 I16 T19 R21 F85 R87 Y92 R104 F110
BS02	rna	1S	K11 R15 K19 R25 F29 R30 S31 L32 K33 H34 Y36 Q38 G45 V46 T47 S50 L54 N61 K62 T63 K93 H95 G96 R97	K9 R13 K17 R23 F27 R28 S29 L30 K31 H32 Y34 Q36 G43 V44 T45 S48 L52 N59 K60 T61 K91 H93 G94 R95
BS03	MG	1S	R15 D88 G90	R13 D86 G88
BS04	MG	1S	K62 R97	K60 R95

Gene Ontology

	Molecular Function
GO:0003735	structural constituent of ribosome
GO:0008097	5S rRNA binding
GO:0019843	rRNA binding

	Biological Process
GO:0006412	translation

	Cellular Component
GO:0005737	cytoplasm
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	Q5SHQ4\|RL18_THET8 Large ribosomal subunit protein uL18 (Gene Name=rplR)