Structure of PDB 8k2a Chain SE

Receptor sequence

>8k2aSE (length=320) Species: 9606 (Homo sapiens)

SFFTKLTADELWKGALAETGLNRGQIIGEGRYGFLWPGLNVPLVQTIAQR
SKEEQEKVEADMIQQREEWDRKKKMKVKRERGWSGNSWGGISLGPPDPGP
CGETYEDFDTRILEVRNVFTMTAKEGRKKSIRVLVAVGNGKGAAGFSIGK
ATDRMDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRFKRTHIKMKKQPK
GYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQ
QLADKKGLHVVEIREECGPLPIVVASPRGPLRKDPEPEDEVPDVKLDWED
VKTAQGMKRSVWSNLKRAAT

3D structure

• PDB: 8k2a Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: SE
• Resolution: 2.9 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	SE	K100 G101 A104 T106 G107 R136 R191 S194 G195 N196 R226 V228 F229 T230 M231 T232 A233 K234 R237 R242 F256 I258 K260 R269 R274 R297 F298 K299 R300 C316 H317 R318 A334 K335 V336 S339 N341 L343 Q347 W408 R419 V421 W422 R427	K13 G14 A17 T19 G20 R31 R81 S84 G85 N86 R116 V118 F119 T120 M121 T122 A123 K124 R127 R132 F146 I148 K150 R159 R164 R187 F188 K189 R190 C206 H207 R208 A224 K225 V226 S229 N231 L233 Q237 W298 R309 V311 W312 R317

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation
• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005763 mitochondrial small ribosomal subunit
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2a, PDBe:8k2a, PDBj:8k2a
• PDBsum: 8k2a
• PubMed: 38942792
• UniProt: P82675|RT05_HUMAN Small ribosomal subunit protein uS5m (Gene Name=MRPS5)