Structure of PDB 8ev6 Chain 1F

Receptor sequence

>8ev61F (length=202) Species: 300852 (Thermus thermophilus HB8)

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

3D structure

• PDB: 8ev6 Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
• Chain: 1F
• Resolution: 2.946 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 W34 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 T53 R54 G55 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 R72 R74 H75 G76 P81 I82 F83 V84 G85 V88 V89 F90 P92 R95 Y99 T100 P102 K103 K104 V105 R106 G134 K135 T136 R165 N169 L170 P171 L176 G180 N182 Y184 R205	N24 H26 L27 W29 R33 Q35 L36 K38 R39 R40 R41 T43 A44 S45 T46 T48 R49 G50 V52 A53 Y54 S55 G56 R57 K58 Q62 K63 H64 R67 R69 H70 G71 P76 I77 F78 V79 G80 V83 V84 F85 P87 R90 Y94 T95 P97 K98 K99 V100 R101 G129 K130 T131 R160 N164 L165 P166 L171 G175 N177 Y179 R200
BS02	MG	1F	R45 G47	R40 G42
BS03	MG	1F	A58 Y59	A53 Y54
BS04	MG	1F	L170 V173	L165 V168

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:8ev6, PDBe:8ev6, PDBj:8ev6
• PDBsum: 8ev6
• PubMed: 37537169
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)