Structure of PDB 8bqx Chain BA Binding Site BS01

Receptor Information

>8bqx Chain BA (length=386) Species: 4932 (Saccharomyces cerevisiae)

SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKA
GMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRS
LTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARI
KKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEK
TVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVAC
IGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKAL
EEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL

Ligand information

>8bqx Chain BQ (length=3301)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguagugagagccuuggucagacgcagcgggcgu
gcuuguggacugcuugguggggcuugcucugcuaggcggacuacuugcgu
gccuuguuguagacggccuuggucuugcuacaauuaacgaucaacuuaga
acugguacggacaaggggaaucugacugucuaauuaaaacauagcauugc
gauggucagaaagugauguugacgcaaugugauuucugcccagugcucug
aaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggaguaa
cuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacgc
gcaugaauggauuaacgagauucccacugucccuaucuacuaucuagcga
aaccacagccaagggaacgggcuuggcagaaucagcggggaaagaagacc
cuguugagcuugacucuaguuugacauugugaagagacauagagggcuac
cuuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuuc
cacguucuagcauucaaggucccauucggggcugauccggguugaagaca
uugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacg
cagauguccuaaggggggcucauggagaacagaaaucuccaguagaacaa
aaggguaaaagcccccuugauuuugauuuucagugugaauacaaaccaug
aaaguguggccuaucgauccuuuagucccucggaauuugaggcuagaggu
gccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguuca
uagcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccg
aagcagaauucgguaagcguuggauuguucacccacuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaa
uguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgg
auaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccau
ccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgc
ggugauuucuuugcuccacacaauauagauggauacgaauaaggcguccu
uguggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaa
ggccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaa
aucauuuguauacgacuuagauguacaacgggguauuguaagcaguagag
uagccuuguuguuacgaucugcugagauuaagccuuuguugucugauuug
u

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(..<<<<<<)))))..]]]...............................
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<<<<........>>>><<<<<<....<<<<<<.<<<<<<..<<<...<<<
<.....>>>>...>>>...<<....>>.......<<<<<..<<<<<....
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>>>>>>.>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>
>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>.
.>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<....<<.<<
<<<<<.....<<<....<<<..<.<<<<...<<<<<<.....>>>>>>.>
>>>.>..>>>..>.>>.....>>>>>...<<<<.<<<<.<......>>>>
>.>>>>.....>>>>..>>>>>>>>.>>..<<<<.<<<<<.....>>>>>
.>>>>....<<<......>>>...<<<<<<<..<<<<(((.....<<<<<
<.....<<..........<<<.<<<<<<<<<<.......<<<<<.<<<..
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>>>>>><<.....<<.....<<<<<<.......>>>>>><<<<.....<<
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..>>>.......<<<<<<...<<<<.<<<<<<<.<<<<<<<<<<..{{{.
.>>>>>><...<<<<<....<<<<<<....<<<.....>>>....>>>>>
>.....>>>>>....><<<<<<<<....>>>>>>>>>>>>...>>>>>>>
.>>>>.........>>>>>>..........>>>..>>>>>>>>>>>>..>
>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<...
..<<<<<<<.<<.........<.....<<<<<...............>>>
>><<.<<<<<<<<<...<<<<<<.<....<.<<<.....<.....<<<<<
<<..<<<<.<<<<..<<<<<<<....>>>>>>>..>>>>.>>>>..>>>>
>>>......>.....>>>..>..>.>>>>>>........>>>..>>>>>>
.>>............<<<<<<<<<..<<<.........>>>..<<<<<<<
....<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<..
...<<....<<<<<....>>>>.>...>>..>>>>..>>>>><<<<<<..
.....>>>>>>........<...........<<<<<.......>>>>>..
...>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>..
..>>....<<<<<........>>>>>....[[[[[..{{{.{{......[
[[[.{{[[[[..<<<<<.<<<<<<<<..<<<<<<<<<<<<<<<<......
>>>>>>.>>>>>>>>>>...<<<<<.....<<<<..<<<<........>>
>>...............<<<<<<....>>>>>>..>>>>..>>>>>....
.>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<...........>
>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<..
.(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<.
...>>>.>>))).......((((((..((((.>>>>>>))))))))))..
........]]]]..}}]]]].......<<.<.<.<<<<<<...<<.....
..>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<<<<<
<<......>>>>>>>...>.<<<.........>>>.....>>>>>..>..
.>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]]...
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<<...<<<<....<<<<<<<<<<}}}.>>>>>..>>>>>...>>>>..>>
>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>....>>
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.>>>..>.>>>>>.>>>>>>.............>>.>>>.>>>>>>..<<
<<<.<.............>.....<<<<<<<<<.<<<....<<<<.<..<
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Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bqx The dynamic architecture of Map1- and NatB-ribosome complexes coordinates the sequential modifications of nascent polypeptide chains.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): S2 H3 R4 K5 E7 A8 R10 H11 G12 H13 G15 L17 P18 R19 K20 R21 R26 R28 K30 A31 M53 T54 T55 R62 S65 A75 Y92 T95 R97 L99 R100 S101 T103 T104 W106 R116 R117 F118 Y119 K120 N121 Y123 K124 S125 K126 K128 K132 R150 K153 Y154 R159 Q173 K174 K175 A179 E180 T221 K222 G223 H224 G225 F226 G228 H231 R232 K236 K237 R240 K241 T242 H243 R244 G245 L246 R247 K248 A250 C251 I252 G253 A254 W255 H256 P257 H259 V260 M261 W262 S263 R266 A267 Q269 R270 S274 R275 T276 N279 M308 G309 H313 E316 C327 I328 P329 N331 R332 K333 R334 Y343 R348 S363 K364 F365 G366 K367 K376 M380 L383 K384 K385
• Binding residue (residue number reindexed from 1): S1 H2 R3 K4 E6 A7 R9 H10 G11 H12 G14 L16 P17 R18 K19 R20 R25 R27 K29 A30 M52 T53 T54 R61 S64 A74 Y91 T94 R96 L98 R99 S100 T102 T103 W105 R115 R116 F117 Y118 K119 N120 Y122 K123 S124 K125 K127 K131 R149 K152 Y153 R158 Q172 K173 K174 A178 E179 T220 K221 G222 H223 G224 F225 G227 H230 R231 K235 K236 R239 K240 T241 H242 R243 G244 L245 R246 K247 A249 C250 I251 G252 A253 W254 H255 P256 H258 V259 M260 W261 S262 R265 A266 Q268 R269 S273 R274 T275 N278 M307 G308 H312 E315 C326 I327 P328 N330 R331 K332 R333 Y342 R347 S362 K363 F364 G365 K366 K375 M379 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:8bqx, PDBe:8bqx, PDBj:8bqx
• PDBsum: 8bqx
• PubMed: 37079644
• UniProt: P14126|RL3_YEAST Large ribosomal subunit protein uL3 (Gene Name=RPL3)