Structure of PDB 8ud6 Chain 1U

Receptor sequence

>8ud61U (length=116) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQ

3D structure

• PDB: 8ud6 An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance
• Chain: 1U
• Resolution: 2.7 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	1U	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 W61 I62 N66 R70 N75 Y76 S77 H81 D91 R92 K93	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 W60 I61 N65 R69 N74 Y75 S76 H80 D90 R91 K92
BS02	MG	1U	K5 T6 G7	K4 T5 G6
BS03	MG	1U	R12 K13	R11 K12
BS04	MG	1U	G7 V8 R10 R11	G6 V7 R9 R10
BS05	MG	1U	Y47 R50 K51	Y46 R49 K50
BS06	MG	1U	G26 K30	G25 K29
BS07	MG	1U	V63 A67	V62 A66
BS08	MG	1U	L18 K22 S29	L17 K21 S28
BS09	MG	1U	T38 A41	T37 A40
BS10	MG	1U	F40 G43 N44	F39 G42 N43

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:8ud6, PDBe:8ud6, PDBj:8ud6
• PDBsum: 8ud6
• PubMed: 38359125
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)