Structure of PDB 6woo Chain C Binding Site BS01

Receptor Information

>6woo Chain C (length=359) Species: 4932 (Saccharomyces cerevisiae)

RPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAV
SEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAP
TKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLVV
STDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQR
RGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTE
AAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRPA
GQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPA
AVFTETLKH

Ligand information

>6woo Chain 5 (length=3271)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacgccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
agugagggccuuggucagacgcagcguuguagacggccuugguaggucuc
uuguagaugcuacaauuacgaucaacuuagaacugguacggacaagggga
aucugacugucuaauuaaaacauagcauugcgauggucagaaagugaugu
ugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaaau
ucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaaggua
gccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaacgag
auucccacugucccuaucuacuaucuagcgaaaccacagccaagggaacg
ggcuuggcagaaucagcggggaaagaagacccuguugagcuugacucuag
uuugacauugugaagagacauagaggguguagaauaagugggagcuucgg
cgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaaugaag
cggagcuggaauucauuuuccacguucuagcauucaaggucccauucggg
gcugauccggguugaagacauugucagguggggaguuuggcuggggcggc
acaucuguuaaacgauaacgcagauguccuaaggggggcucauggagaac
agaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuu
cagugugaauacaaaccaugaaaguguggccuaucgauccuuuagucccu
cggaauuugaggcuagaggugccagaaaaguuaccacagggauaacuggc
uuguggcagucaagcguucauagcgacauugcuuuuugauucuucgaugu
cggcucuuccuaucauaccgaagcagaauucgguaagcguuggauuguuc
acccacuaauagggaacgugagcuggguuuagaccgucgugagacagguu
aguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuaguac
gagaggaacaguucauucggauaauugguuuuugcggcugucugaucagg
cauugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagu
cagaauccaugcuagaacgcggugauuucuuugcuccacacaauauagau
ggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagc
aacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaau
gucauuuugcguggggauaaaucauuuguauacgacuuagauguacaacg
ggguauuguaagcaguagaguagccuuguuguuacgaucugcugagauua
agccuuuguugucugauuugu

..........................<<<<<<.....<......>.....
.>>>>>.>.........<<....>>..<<<<<......<<.....>>...
..>>>>>..<<<...<.......<<.<<<<<<...>>>>>>.>>......
.>.....<<<<<<<.<<<<<<<<<<<<<<<<<<<<.....<<<<......
>>>>.(.......<<<......)>>>....>>>>>>>>..>>>>>>>>..
..>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<
<<<..((((((>>>>>..>>>.............................
.....<<....>>...............<<<<....>>>>..........
........................<<<<<.<<<<<....<<<<<<<.<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<<<..>>>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<
<....<<<<..<<.<<<<.....>>>>.>>>>>>....>>>..>.>>...
..>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>
>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>
>>...<<<<<<<..<<<<(((.....<<<<<<......<..........<
<<.<<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>
>.........<<......>>...>>>>>...>>>>>>>>>>>>>......
....))).>....>>>>>>.>>>>..>>>>>>><<<<<<<<<........
.>>>>>>>>>....>>>>>><.<<<<<<<<.<<......<<<<.<<<<..
..>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<....
.<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<
<.....>>.>>>>>>....((<<<<<<...<<....<<<....>>>....
....<<<<<<........>>>>>>....>>....>>...<<<<<......
..>>>>>))<<<<.<<<<<<<.....<<<....>>>.......<<<<<<.
..<<<<.<<<<<<<<<<<<<<<<<<..[[[..>>>>>><...<<<<<...
.<<<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<
<<<<<....>>>>>>>>>>>>.>.>>>>>>>.>>>>.........>>>>>
>..........>>>..>>>>>>>>>>>>..>>.....<<......>>>>>
>>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.......
..<.....<<<<<.....<..>......>>>>><<.<<<<<<<<<<<...
........<<..<<<<.....<<<..>>>.....>>>>..>>........
..................>>>>>..>>>>>>.>>............<<<<
<<<<<..<<<.........>>>..<<<<<<<....<<<<.....>>>>..
....>>>>>>>...<<..<<<..<<<<<..<..<<<.....<<<<....>
>>>.....>>>>.>>>..>>>>>.<<<<<.......>>>>>.........
<...........<<<<<.......>>>>>.....>.....>>....>>.>
>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....<<<<<......
..>>>>>....<<<<<..<<<.<<......<<<<.<<<<<<..<<<<<.<
<<<<<<<..<<<<<<......<<<<...........<<<..<.<<....>
>............>.>>>..>>>>.......>>>>>>...<<<<<.....
<<<<................................<<.<<.......>>
.>>..>>>>..>>>>>.....>>>>>>>>..>>>>>...<<<.....>>>
..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<..
.....>>>>>>.....<<...(((>>....>>>>>>>...<<<.<<<<<.
......>>>>.>>>>.<<<....>>>.>>)))......<<<<<<<..<<<
<.))))))>>>>>>>>>>>.........>>>>..>>>>>>.......<<.
<.<.<<<<<<...<<.......>>...>>>>>>...>>.>.>.......<
<<<<.<<<<<<..<.<<<<<<<......>>>>>>>...>.<<<.......
..>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>
....>>..>>>.>>>>>....<<<<<<<<..<<<<...<<<<<<......
.........>>>>>>..<<<<<...<<<<....<<<<<<<<<<]]].>>>
>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<...........>>>
>>...>>>>.>>>>....>>>>>>>>.......<<<<<<.<<<.<<....
<<..........<<<<<<.....>>>>>>......>>.......<<<<<<
...<<<<<.<..<<<......>>>..>.>>>>>.>>>>>>..........
...>>.>>>.>>>>>>..<<<<<.<.............>.....<<<<<<
<<<.<<<....<<<<....<<<<<......>>>>>...>>>>...>>>..
..>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6woo An active role of the eukaryotic large ribosomal subunit in translation initiation fidelity.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): R31 I34 H36 T40 K44 N45 K46 R47 Q48 Y50 V52 S53 A56 H58 Q59 T60 S61 S64 T67 G68 A70 V71 A72 R73 P75 V77 G78 G80 G81 T82 R84 Q87 G88 N92 M93 C94 R95 G96 R98 M99 F100 A101 K104 W106 R107 K108 V111 K112 V113 N114 H115 N116 E117 K118 R119 Y120 R138 G139 R141 K161 T162 K180 K183 K186 R188 A189 G190 K191 K193 Y194 R195 R197 W199 R202 R203 Y209 V216 K217 R220 N221 P223 T227 A228 S232 N234 P240 G241 H243 K271 V272 N291 R300 A302 G303 Q304 A305 Q307 K308 R309 V312 L313 K315 N320 Q322 R326 N328 A331 F334 A335 S341 K342 K343 K346 F355 L359
• Binding residue (residue number reindexed from 1): R29 I32 H34 T38 K42 N43 K44 R45 Q46 Y48 V50 S51 A54 H56 Q57 T58 S59 S62 T65 G66 A68 V69 A70 R71 P73 V75 G76 G78 G79 T80 R82 Q85 G86 N90 M91 C92 R93 G94 R96 M97 F98 A99 K102 W104 R105 K106 V109 K110 V111 N112 H113 N114 E115 K116 R117 Y118 R136 G137 R139 K159 T160 K178 K181 K184 R186 A187 G188 K189 K191 Y192 R193 R195 W197 R200 R201 Y207 V214 K215 R218 N219 P221 T225 A226 S230 N232 P238 G239 H241 K269 V270 N289 R298 A300 G301 Q302 A303 Q305 K306 R307 V310 L311 K313 N318 Q320 R324 N326 A329 F332 A333 S339 K340 K341 K344 F353 L357

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:6woo, PDBe:6woo, PDBj:6woo
• PDBsum: 6woo
• UniProt: P10664|RL4A_YEAST Large ribosomal subunit protein uL4A (Gene Name=RPL4A)