Structure of PDB 6y57 Chain LJ

Receptor sequence

>6y57LJ (length=167) Species: 9606 (Homo sapiens)

NPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRS
FGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGI
QEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISK
EEAMRWFQQKYDGIILP

3D structure

• PDB: 6y57 Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes.
• Chain: LJ
• Resolution: 3.5 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	LJ	C21 N23 C25 G27 S51 R54 S59 F60 I62 H71 N98 S100 D101 T102 G106 F107 G108 I109 Q110 G127 L128 D129 Y131 K145	C12 N14 C16 G18 S42 R45 S50 F51 I53 H62 N89 S91 D92 T93 G97 F98 G99 I100 Q101 G118 L119 D120 Y122 K136
BS02	rna	LJ	M12 R13 Q46 T47 C72 T73 R75 P137 G138 S140 I141 D143 K144 R147 C150 K154 H155	M3 R4 Q37 T38 C63 T64 R66 P128 G129 S131 I132 D134 K135 R138 C141 K145 H146

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:6y57, PDBe:6y57, PDBj:6y57
• PDBsum: 6y57
• PubMed: 32268098
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)