Structure of PDB 8k2d Chain LY

Receptor sequence

>8k2dLY (length=124) Species: 4932 (Saccharomyces cerevisiae)

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKGGK

3D structure

• PDB: 8k2d Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: LY
• Resolution: 3.2 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	LY	A2 Q4 S5 V8 S9 S10 D11 R12 K14 R16 Y19 V29 K37 K46 R60 G61 S62 K89 V90 N91 H100 S102 K103 R121	A1 Q3 S4 V7 S8 S9 D10 R11 K13 R15 Y18 V28 K36 K45 R59 G60 S61 K88 V89 N90 H99 S101 K102 R120
BS02	rna	LY	R12 R13 R16 K17 F20 P23 S24 R51 R52 V73 Y74 R75 L111 D112 K113 D114	R11 R12 R15 K16 F19 P22 S23 R50 R51 V72 Y73 R74 L110 D111 K112 D113

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0032991 protein-containing complex
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2d, PDBe:8k2d, PDBj:8k2d
• PDBsum: 8k2d
• PubMed: 38942792
• UniProt: P05743|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)