Structure of PDB 5vp2 Chain 2U

Receptor sequence

>5vp22U (length=116) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQ

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	2U	P2 R3 A4 K5 T6 G7 V8 R10 R11 R12 K13 H14 K15 K16 K19 K22 G23 Y24 W25 G26 L27 R28 K30 S31 F32 R33 K34 R36 E37 A42 Y45 A46 Y47 H49 R50 K51 R52 R53 K54 R55 F57 R58 R59 I62 V63 N66 R70 N75 Y76 S77 H81 D91 R92	P1 R2 A3 K4 T5 G6 V7 R9 R10 R11 K12 H13 K14 K15 K18 K21 G22 Y23 W24 G25 L26 R27 K29 S30 F31 R32 K33 R35 E36 A41 Y44 A45 Y46 H48 R49 K50 R51 R52 K53 R54 F56 R57 R58 I61 V62 N65 R69 N74 Y75 S76 H80 D90 R91
BS02	MG	2U	G43 Y47	G42 Y46
BS03	MG	2U	R52 D56	R51 D55
BS04	MG	2U	G7 V8 V9 R10 R11	G6 V7 V8 R9 R10

Gene Ontology

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

	Biological Process
GO:0000027	ribosomal large subunit assembly
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	P60491\|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)