Structure of PDB 8ud7 Chain 1F

Receptor sequence

>8ud71F (length=202) Species: 300852 (Thermus thermophilus HB8)

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

3D structure

• PDB: 8ud7 An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance
• Chain: 1F
• 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	1F	N29 H31 L32 E35 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 T53 R54 G55 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 P81 I82 F83 V84 G85 V88 V89 F90 P92 P94 R95 Y99 T100 P102 K103 K104 R106 K108 G134 K135 T136 R165 R168 N169 P171 L176 E179 G180 N182 Y184 R205	N24 H26 L27 E30 R33 Q35 L36 K38 R39 R40 R41 T43 A44 S45 T46 T48 R49 G50 V52 A53 Y54 S55 G56 R57 K58 Q62 K63 H64 G66 R67 A68 R69 H70 G71 P76 I77 F78 V79 G80 V83 V84 F85 P87 P89 R90 Y94 T95 P97 K98 K99 R101 K103 G129 K130 T131 R160 R163 N164 P166 L171 E174 G175 N177 Y179 R200
BS02	MG	1F	T51 K52	T46 K47
BS03	MG	1F	G61 R62	G56 R57
BS04	MG	1F	R72 A73	R67 A68
BS05	MG	1F	G76 D77	G71 D72
BS06	MG	1F	S50 T51	S45 T46
BS07	MG	1F	V57 Y59	V52 Y54
BS08	MG	1F	R168 L170	R163 L165
BS09	MG	1F	K63 W65 P66 Q67 R74 H75	K58 W60 P61 Q62 R69 H70
BS10	MG	1F	R54 D77	R49 D72
BS11	MG	1F	R164 T175	R159 T170
BS12	MG	1F	R117 E190	R112 E185

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ud7, PDBe:8ud7, PDBj:8ud7
• PDBsum: 8ud7
• PubMed: 38359125
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)