Structure of PDB 8scb Chain C Binding Site BS01

Receptor Information

>8scb Chain C (length=362) Species: 9986 (Oryctolagus cuniculus)

ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQP
YAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRM
FAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELP
LVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRR
IQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLAPGGHVGRFCI
WTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRV
ERAAAALAAKSD

Ligand information

>8scb Chain 5 (length=3530)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccaccccggcgccggggggcccaaguccuucuga
ucgaggcccagcccguggacggugugaggccgguagcggcccccggcgcg
ccgggcccgggucuucccggagucggguugcuugggaaugcagcccaaag
cgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauaguc
aacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaa
gagggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgc
ccggaggauucaacccggcggcgcgguccggccgugccggcggggcggau
cucccgcucccgucggcgggggaccgccccccggccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggccccggcggggaagguggcccgggggccccggguguuacag
ccccgccccggcagcagcagcucgccgaaucccggggccgagggagcgag
acccgugcgccgcgcucuccccccucgggggggccgggccaccccuccca
cggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgc
cgucgggcccggggggccacgcgagcgcacggggucggcggcgaugucgg
cuacccacccgacccgucuugaaacacggaccaaggagucuaacacgugc
gcgagucgggggcuacgaaagccgccguggcgcaaugaaggugaaggccg
gcggcgcgccgccggccgaggugggaucccgaggccuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcgaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccaaaguuucccucaggauagcuggcgcucuccgcaguu
uuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaa
ccuauucucaaacuuuaaauggguaagaagcccggcucgcugguguggag
ccgggcguggaaugcgagugccuagugggccacuuuugguaagcagaacu
ggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgc
ucaucagaccccagaaaagguguugguugauauagacagcaggacggugg
ccauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgcuacg
ccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcg
ggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaaua
uucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaaca
gcaguugaacaugggucagucgguccugagagaugggcgagcgccguucc
gaagggacgggcgauggccuccguugcccucagccgaucgaaagggaguc
ggguucagauccccgaauccggaguggcggagaugggcgccgcgaggcgu
ccagugcgguaacgcgaccgaucccggagaagccggcgggagccccgggg
agaguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcc
ccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggcgucc
ggugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucuc
gcgccgggccguacccauauccgcagcaggucuccaaggugaacagccuc
uggcauguuggaacaauguagguaagggaagucggcaagccggauccgua
acuucgggauaaggauuggcucuaagggcuggcagccgacuuagaacugg
ugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaagg
cccgcggcggguguugacgcgaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaug
acucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaug
aauggaugaacgagauucccacugucccuaccuacuauccagcgaaacca
cagccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguu
gagcuugacucuagucuggcacggugaagagacguuuuuucacugacccg
gugaggcgggggggcgagccgggcucucgcuucuggcgccaagcgcccgg
ccggccgggcgcgacccgcuccggggacagugccagguggggaguuugac
uggggcgguacaccugucaaacgguaacgcagguguccuaaggcgagcuc
agggaggacagaaaccucccguggagcagaagggcaaaagcucgcuugau
cuugauuuucaguacgaauacagaccgugaaagcggggccucacgauccu
ucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacaggg
auaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuugauc
cuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugauguguuguugccaugguaaucc
ugcucaguacgagaggaaccgcagguucagacauuugguguaugugcuug
gcugaggagccaauggggcgaagcuaccaucugugggauuaugacugaac
gccucuaagucagaaucccgcccaggcggaacgauagcgccggagccucg
guuggccucggauagccggucccccgccgggguccggugcggagagcccu
ucgucccgggaaacgggcggccggaaagggggccgcccucucgcccguca
cgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgacc
ugcuucugggucgggguuucguacguagcagagcagcugcugcgaucuau
ugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8scb Structure and consequences of eRF1 glued to the ribosomal decoding center
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): A2 A4 R5 P6 K29 R33 I36 N38 F39 H41 T42 N43 R45 K46 N47 N48 R49 Q50 Y52 V54 S55 A58 H60 Q61 T62 S63 S66 T69 G70 A72 V73 A74 R75 P77 R80 G83 T84 R86 Q89 N94 M95 C96 R97 G98 R100 M101 F102 A103 K106 W108 R109 R110 R114 N116 T117 T118 Q119 K120 R121 K140 R143 K163 T164 K165 K172 N178 K181 K182 Y184 R188 M189 R190 A191 G192 K193 K195 M196 R197 R199 R201 R204 R205 K219 R222 N223 K234 L235 N236 K239 P242 G243 H245 W267 R268 K274 S275 M281 H282 L285 R291 L293 Q299 R303 A304 P305 R306 K307 I309 H310 R311 R312 L314 K316 N317 K320 N321 L322 R323 L326 K327 K333 M335 R336 T339 R342 Q343 N346 H347 R350
• Binding residue (residue number reindexed from 1): A1 A3 R4 P5 K28 R32 I35 N37 F38 H40 T41 N42 R44 K45 N46 N47 R48 Q49 Y51 V53 S54 A57 H59 Q60 T61 S62 S65 T68 G69 A71 V72 A73 R74 P76 R79 G82 T83 R85 Q88 N93 M94 C95 R96 G97 R99 M100 F101 A102 K105 W107 R108 R109 R113 N115 T116 T117 Q118 K119 R120 K139 R142 K162 T163 K164 K171 N177 K180 K181 Y183 R187 M188 R189 A190 G191 K192 K194 M195 R196 R198 R200 R203 R204 K218 R221 N222 K233 L234 N235 K238 P241 G242 H244 W266 R267 K273 S274 M280 H281 L284 R290 L292 Q298 R302 A303 P304 R305 K306 I308 H309 R310 R311 L313 K315 N316 K319 N320 L321 R322 L325 K326 K332 M334 R335 T338 R341 Q342 N345 H346 R349

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8scb, PDBe:8scb, PDBj:8scb
• PDBsum: 8scb
• PubMed: 38172604
• UniProt: G1SVW5|RL4_RABIT Large ribosomal subunit protein uL4 (Gene Name=RPL4)