Structure of PDB 6woo Chain B Binding Site BS01

Receptor Information

>6woo Chain B (length=384) Species: 4932 (Saccharomyces cerevisiae)

SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKA
GMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRS
LTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARI
KKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEK
TVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVAC
IGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKAL
EEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKK

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): S2 H3 R4 K5 Y6 E7 A8 P9 R10 H11 G12 H13 L14 G15 L17 P18 R19 K20 R21 I25 R26 R28 K30 A31 K50 M53 T54 T55 R62 S65 A75 Y92 V93 T95 P96 R97 L99 R100 S101 L102 T103 T104 R117 F118 Y119 K120 N121 Y123 K124 S125 K126 K128 F130 K132 Y133 K153 Y154 R159 Q173 K174 K175 E180 T221 K222 G223 H224 G225 F226 G228 H231 K236 K237 R240 K241 T242 H243 R244 G245 R247 K248 A250 C251 I252 G253 A254 W255 H256 P257 A258 H259 V260 W262 S263 R266 A267 Q269 R270 Y272 S274 R275 T276 I278 N279 G309 V312 H313 G315 G326 C327 I328 P329 R332 K333 R334 R339 L342 Y343 S363 K364 F365 G366 K367 K376 M380 G381 L383 K384 K385
• Binding residue (residue number reindexed from 1): S1 H2 R3 K4 Y5 E6 A7 P8 R9 H10 G11 H12 L13 G14 L16 P17 R18 K19 R20 I24 R25 R27 K29 A30 K49 M52 T53 T54 R61 S64 A74 Y91 V92 T94 P95 R96 L98 R99 S100 L101 T102 T103 R116 F117 Y118 K119 N120 Y122 K123 S124 K125 K127 F129 K131 Y132 K152 Y153 R158 Q172 K173 K174 E179 T220 K221 G222 H223 G224 F225 G227 H230 K235 K236 R239 K240 T241 H242 R243 G244 R246 K247 A249 C250 I251 G252 A253 W254 H255 P256 A257 H258 V259 W261 S262 R265 A266 Q268 R269 Y271 S273 R274 T275 I277 N278 G308 V311 H312 G314 G325 C326 I327 P328 R331 K332 R333 R338 L341 Y342 S362 K363 F364 G365 K366 K375 M379 G380 L382 K383 K384

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006414 translational elongation
• GO:1990145 maintenance of translational fidelity

Cellular Component

• 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: P14126|RL3_YEAST Large ribosomal subunit protein uL3 (Gene Name=RPL3)