Structure of PDB 4v88 Chain DC

Receptor sequence

>4v88DC (length=361) Species: 559292 (Saccharomyces cerevisiae S288C)

SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYA
VSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFA
PTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLV
VSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQ
RRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWT
EAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRP
AGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKP
AAVFTETLKHD

3D structure

• PDB: 4v88 The structure of the eukaryotic ribosome at 3.0 angstrom resolution.
• Chain: DC
• Resolution: 3.0 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	DC	I34 H36 T40 K44 N45 K46 R47 Q48 Y50 V52 S53 E54 A56 H58 Q59 T60 S61 T67 G68 R69 A70 V71 R73 I74 P75 R76 G78 G80 G81 T82 R84 Q87 N92 M93 C94 R95 G96 R98 M99 F100 A101 K104 W106 R107 K108 V111 K112 N114 H115 N116 E117 K118 R119 R138 R141 K161 T162 K163 L179 K180 K183 K186 L187 R188 A189 G190 K191 K193 Y194 R195 N196 R197 W199 R202 R203 Y209 V216 K217 R220 N221 T227 A228 N234 P240 G241 H243 K271 T287 N291 R300 G303 A305 Q307 K308 R309 V312 L313 K315 N320 Q322 R326 A331 K332 F334 A335 G340 S341 K342 K343 T347 T349 P351 F355 L359	I33 H35 T39 K43 N44 K45 R46 Q47 Y49 V51 S52 E53 A55 H57 Q58 T59 S60 T66 G67 R68 A69 V70 R72 I73 P74 R75 G77 G79 G80 T81 R83 Q86 N91 M92 C93 R94 G95 R97 M98 F99 A100 K103 W105 R106 K107 V110 K111 N113 H114 N115 E116 K117 R118 R137 R140 K160 T161 K162 L178 K179 K182 K185 L186 R187 A188 G189 K190 K192 Y193 R194 N195 R196 W198 R201 R202 Y208 V215 K216 R219 N220 T226 A227 N233 P239 G240 H242 K270 T286 N290 R299 G302 A304 Q306 K307 R308 V311 L312 K314 N319 Q321 R325 A330 K331 F333 A334 G339 S340 K341 K342 T346 T348 P350 F354 L358
BS02	rna	DC	A49 A51 S53 K193 Y194	A48 A50 S52 K192 Y193
BS03	OHX	DC	K144 I145 P146	K143 I144 P145
BS04	MG	DC	T122 L235	T121 L234

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v88, PDBe:4v88, PDBj:4v88
• PDBsum: 4v88
• PubMed: 22096102
• UniProt: P10664|RL4A_YEAST Large ribosomal subunit protein uL4A (Gene Name=RPL4A)