Structure of PDB 8ud7 Chain 1X

Receptor sequence

>8ud71X (length=95) Species: 300852 (Thermus thermophilus HB8)

MKTAYDVILAPVLSEKAYAGFAEGKYTFWVHPKATKTEIKNAVETAFKVK
VVKVNTLHVRGKKKRLGRYLGKRPDRKKAIVQVAPGQKIEALEGL

3D structure

• PDB: 8ud7 An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance
• Chain: 1X
• Resolution: 2.55 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	1X	S14 K16 K25 H31 T35 K36 T37 K40 N41 K53 N55 T56 L57 H58 R60 K62 K63 K64 R65 L66 Y69 L70 G71 K72 R73 P74 D75 K78 I80	S14 K16 K25 H31 T35 K36 T37 K40 N41 K53 N55 T56 L57 H58 R60 K62 K63 K64 R65 L66 Y69 L70 G71 K72 R73 P74 D75 K78 I80
BS02	MG	1X	T56 K77	T56 K77
BS03	MG	1X	W29 V30 R76 K77	W29 V30 R76 K77
BS04	MG	1X	R73 P74 R76	R73 P74 R76
BS05	MG	1X	V59 R60 G61 P74 D75 R76	V59 R60 G61 P74 D75 R76
BS06	MG	1X	A17 F21 K25 Y26 T27	A17 F21 K25 Y26 T27

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:8ud7, PDBe:8ud7, PDBj:8ud7
• PDBsum: 8ud7
• PubMed: 38359125
• UniProt: Q5SHP0|RL23_THET8 Large ribosomal subunit protein uL23 (Gene Name=rplW)