Structure of PDB 8yop Chain LP

Receptor sequence

>8yopLP (length=153) Species: 9606 (Homo sapiens)

VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDV
TLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESN
AELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT
EKE

3D structure

• PDB: 8yop Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: LP
• Resolution: 2.2 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	LP	V2 R3 Y4 L6 K16 S17 R18 G19 S20 R23 H25 F26 K27 R30 Q34 K37 K43 R62 Y63 N64 G65 G66 G68 R69 A71 Q72 K74 Q75 W78 Q80 R82 W83 P84 K85 K86 K96 N97 S100 N101 L104 Q118 V119 K121 R127 T129 Y130 R131 A132 H133 G134 R135 I136 N137 P138 Y139 M140 S141 S142	V1 R2 Y3 L5 K15 S16 R17 G18 S19 R22 H24 F25 K26 R29 Q33 K36 K42 R61 Y62 N63 G64 G65 G67 R68 A70 Q71 K73 Q74 W77 Q79 R81 W82 P83 K84 K85 K95 N96 S99 N100 L103 Q117 V118 K120 R126 T128 Y129 R130 A131 H132 G133 R134 I135 N136 P137 Y138 M139 S140 S141
BS02	rna	LP	R3 S5 R61 R62 W78 N120 K121 P123 H145	R2 S4 R60 R61 W77 N119 K120 P122 H144

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8yop, PDBe:8yop, PDBj:8yop
• PDBsum: 8yop
• PubMed: 38942792
• UniProt: P18621|RL17_HUMAN Large ribosomal subunit protein uL22 (Gene Name=RPL17)