Structure of PDB 6olg Chain AJ

Receptor sequence

>6olgAJ (length=169) Species: 9606 (Homo sapiens)

ENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVR
SFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFG
IQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRIS
KEEAMRWFQQKYDGIILPG

3D structure

• PDB: 6olg Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.
• Chain: AJ
• 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	AJ	M12 Q46 T47 V49 T73 R75 G138 S140 I141 K144 R147 C150 I151 K154 H155	M4 Q38 T39 V41 T65 R67 G130 S132 I133 K136 R139 C142 I143 K146 H147
BS02	rna	AJ	K19 N23 C25 S51 K52 A53 Y55 F60 N97 N98 S100 D101 G106 F107 G108 Q110 G127 D129 Y131 K145	K11 N15 C17 S43 K44 A45 Y47 F52 N89 N90 S92 D93 G98 F99 G100 Q102 G119 D121 Y123 K137
BS03	rna	AJ	R58 R64	R50 R56

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0031625 ubiquitin protein ligase binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006605 protein targeting
• GO:0010628 positive regulation of gene expression
• GO:0032092 positive regulation of protein binding
• GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
• GO:0034504 protein localization to nucleus
• GO:0042273 ribosomal large subunit biogenesis
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1901798 positive regulation of signal transduction by p53 class mediator
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
• GO:2000435 negative regulation of protein neddylation

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6olg, PDBe:6olg, PDBj:6olg
• PDBsum: 6olg
• PubMed: 31160784
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)