Structure of PDB 8k2b Chain LD

Receptor sequence

>8k2bLD (length=250) Species: 9606 (Homo sapiens)

EPVLRKVELPVPTHRRPVQAWVESLRGFEQERVGLADLHPDVFATAPRLD
ILHQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSP
LWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTVKLAQDDLHIMDSLE
LPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTFNLIP
AVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFP

3D structure

• PDB: 8k2b Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: LD
• Resolution: 3.4 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	LD	R92 H97 M101 K104 N105 R108 Y111 T114 K115 R117 A118 V120 R121 G122 R125 K126 Q130 K131 G132 G134 R135 A136 R137 H138 G139 R142 S143 L145 R147 G148 V151 H153 P155 Y161 Y163 M167 K168 V169 R170 K255 R281 P282 P285	R48 H53 M57 K60 N61 R64 Y67 T70 K71 R73 A74 V76 R77 G78 R81 K82 Q86 K87 G88 G90 R91 A92 R93 H94 G95 R98 S99 L101 R103 G104 V107 H109 P111 Y117 Y119 M123 K124 V125 R126 K211 R237 P238 P241

Gene Ontology

Molecular Function

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

Biological Process

• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2b, PDBe:8k2b, PDBj:8k2b
• PDBsum: 8k2b
• PubMed: 38942792
• UniProt: Q9BYD3|RM04_HUMAN Large ribosomal subunit protein uL4m (Gene Name=MRPL4)