Structure of PDB 8yop Chain LC

Receptor sequence

>8yopLC (length=368) Species: 9606 (Homo sapiens) [Search protein sequence]

MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQ
PYAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGR
MFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPEL
PLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRR
RIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFC
IWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLR
VDKAAAAAAALQAKSDEK

3D structure

PDB

8yop Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.

Chain

Resolution

2.2 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

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	LC	M1 R33 N38 F39 T42 N43 R45 K46 N47 N48 R49 Q50 Y52 V54 S55 A58 G59 H60 Q61 T62 S63 T69 G70 R71 A72 V73 A74 R75 P77 R80 G83 T84 R86 Q89 G90 N94 M95 R97 G98 R100 M101 F102 A103 K106 W108 R109 R110 R114 N116 T118 Q119 K120 R121 Y122 K140 K163 T164 K165 K172 N178 K181 K182 Y184 R188 R190 A191 G192 K193 K195 M196 R197 R199 R201 R204 R205 K219 R222 N223 K234 L235 N236 P242 G243 H245 R268 K274 R291 L293 R303 A304 P305 R306 K307 K308 I309 H310 R311 R312 L314 K316 K320 N321 L322 R323 L326 K327 K333 M335 R336 T339 R342 Q343 N346 H347 R350	M1 R33 N38 F39 T42 N43 R45 K46 N47 N48 R49 Q50 Y52 V54 S55 A58 G59 H60 Q61 T62 S63 T69 G70 R71 A72 V73 A74 R75 P77 R80 G83 T84 R86 Q89 G90 N94 M95 R97 G98 R100 M101 F102 A103 K106 W108 R109 R110 R114 N116 T118 Q119 K120 R121 Y122 K140 K163 T164 K165 K172 N178 K181 K182 Y184 R188 R190 A191 G192 K193 K195 M196 R197 R199 R201 R204 R205 K219 R222 N223 K234 L235 N236 P242 G243 H245 R268 K274 R291 L293 R303 A304 P305 R306 K307 K308 I309 H310 R311 R312 L314 K316 K320 N321 L322 R323 L326 K327 K333 M335 R336 T339 R342 Q343 N346 H347 R350
BS02	rna	LC	P51 A53 V54 S55 T107 K195 M196	P51 A53 V54 S55 T107 K195 M196

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003735	structural constituent of ribosome
GO:0005515	protein binding

	Biological Process
GO:0002181	cytoplasmic translation
GO:0006412	translation

	Cellular Component
GO:0005634	nucleus
GO:0005730	nucleolus
GO:0005737	cytoplasm
GO:0005791	rough endoplasmic reticulum
GO:0005829	cytosol
GO:0005840	ribosome
GO:0005925	focal adhesion
GO:0016020	membrane
GO:0022625	cytosolic large ribosomal subunit
GO:0022626	cytosolic ribosome
GO:0070062	extracellular exosome
GO:1990904	ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:8yop, PDBe:8yop, PDBj:8yop
PDBsum	8yop
PubMed	38942792
UniProt	P36578\|RL4_HUMAN Large ribosomal subunit protein uL4 (Gene Name=RPL4)

[Back to BioLiP]