Structure of PDB 8k2c Chain LG

Receptor sequence

>8k2cLG (length=241) Species: 9606 (Homo sapiens)

KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLK
VPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGK
GDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCR
KMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTN
YNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG

3D structure

• PDB: 8k2c Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: LG
• Resolution: 2.4 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	LG	E33 K34 R35 K37 F39 I41 G42 Q43 D44 Q46 P47 R49 L51 R53 F54 K56 P58 R59 Y60 R62 I69 K72 R73 L74 K75 K107 K110 R113 R132 P133 A138 G139 V140 N141 T142 V161 D162 P163 L166 K187 A188 R192 R196 K197 T198 C199 T200 P244 K245 S246 R249	E8 K9 R10 K12 F14 I16 G17 Q18 D19 Q21 P22 R24 L26 R28 F29 K31 P33 R34 Y35 R37 I44 K47 R48 L49 K50 K82 K85 R88 R107 P108 A113 G114 V115 N116 T117 V136 D137 P138 L141 K162 A163 R167 R171 K172 T173 C174 T175 P219 K220 S221 R224
BS02	rna	LG	T52 W57 Y60 I61 Q64 R65 R89 H159 D160 K185 R189	T27 W32 Y35 I36 Q39 R40 R64 H134 D135 K160 R164

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2c, PDBe:8k2c, PDBj:8k2c
• PDBsum: 8k2c
• PubMed: 38942792
• UniProt: P62424|RL7A_HUMAN Large ribosomal subunit protein eL8 (Gene Name=RPL7A)