Structure of PDB 8p5d Chain LB0 Binding Site BS01

Receptor Information

>8p5d Chain LB0 (length=383) Species: 1358809 (Spraguea lophii 42_110)

SCRNYSAPRHGSLAYCPKKRAKTTKPAIKSFPKDDASKPVHLTGYLAYKV
GMTHVVRLSTRRSKTERVLKETQKEVLDAVTILEVPAMRIFGMVGYKSTV
NGLKAIKTVYAEHLDEQVLARLRKRNSRSSKLMFKLYPQKYENGDIKRDY
ELLKRESDVVRVLAHTQVSKIPSLNLKKAHILEIQLNGGTIEEKIEWAIE
RLEKEIPVSEVFSQQDLIDVIGVTKGKGKEGTTKRFGTTILQHKSRKGKR
KVACIGAWHPANVRRTVARAGQLGFHRRTAQNKKIYMMGNGKTPFSTEYD
LTSKTINPMGGFLRYGNVKSDFIMVKGGIQGPSKRVLALRKAFAPSNLGK
DNEEIVLKFVDASSKKGYGRFQTTEEKKAYFGI

Ligand information

>8p5d Chain L50 (length=2499)

auaccacacacaagggaucguuuggcuccugggacgaggaagggcgcagc
agagagcgauaugugugggagcagcagcaaugaccacacguccccgaaua
cagcauagugcuggaguacuccuuggaauuaagcauaugaguaaaggaag
gaaaagaaacuaacgaggauucccguaguagcggcgagugaacagggaac
aguccaacaguguaauucucaaaugagaaguugucaaaaggaagaagaug
ugaaucagaaagaaaagcugaacgauacagggugauagucccguaguguc
uucuuacauacggugaguagcugugcucgguaaugcacagugaagaggug
gcagugugcaucuaagacuaaauacaacaggagaccgauagcaaagaagu
agguugaccgaaaacagugaaauuguguguggacccgaauggaucgggcc
cgucuugaaacacggaccaaggagugcacauacacugcaaguugagcaga
ggaagucugugaggcguagugaagacggaaagcagugugagugcgacccg
auagacuugugaacuauaccuuguugcugugaaggcuggcgaaagccagc
uggaggcggcaagccguauugaucugcaaaucauuggcguaagcagggua
uaggggcgaaagaccaaucgaacagucuaguugcugguucccuccgaaau
gucuaucaggacagcgcgcacgcagagagaagcaagguagagcaugggcc
gguauccuuaaggagacggacgaacugcgaaugugcuuuucuucuaugca
agcguagugggcgaguucugguaagcaggacuggcgaagaggaaugaacc
uggcacugugcuaaggaacccaaugucuggacagagaccgaaagagguag
gugaauaaaauucaucugcucugaaaauugauggcgcuuaccagacaucc
gaugcacaguuagcagguaggagggcgugugucuacuggcgaagguaccg
agugaucggugguggagguagaugcagagcagaucuuggugguaguagcg
auaauuugucuucagcggcaaagacugaggaggagaaggguuucuucuca
uaagaagagugagccgggucuaagcgaguguguagaagcaugagcgaagg
agaaacagguugauauuccugugccugugcugucguacggcaacguguau
uagcuugucgacacgaacaucuagacaaagcagaaacaccuuuucuguuc
aaggggaaaaagaccacugagacggaucaucuggcgacgugguuuuauau
cugugaccaggccugagccugguuuguugaggauggucguccaugaaaag
acaacuauauggcagcacaguccguaccaaccguaucaggacuccaaggu
gaagagccucuaguggauguuuuacacauguaagggaauucggcaaaaug
gaugcguaacuucgggagaaguauugguucaauugugaacucauugugac
aaggggaaucugacuguuuaguaaaaacauagcuucaugaagagagauga
agugaguucugcccggugcucggucgugacacggaggaaaugccagaaag
cacggguuaacggcgggaguaacuaugacucucuuaagguagccaaacgc
cucgucauuuaaauggugacgcgcaugaauggaaugacgagauucccacu
gucccuacauguagacuagcgaacccauuuccaggggaacgggccuggac
ggccagcggggaaagaagacccuguugagcuugacucuaguguggccaag
uugugacgauugaggcgagcgccaugaucaucacgacacacuuguuuaag
gacaaaggccagauggggaguuuggcuggggcgguacgaccacagaauca
gaacguggucgaccgaagguacucacagcgagacgagaacacucguguag
agcauaaggacuaaagagugccugagugugagcacuacugcuugcaugag
gggaaacccgggccuagcgauccuacgcauacgagacacuuguggcgugg
gugucagaaaaguuaccacagggauaacuggcuuguggccgccgagcgua
gaaagcgacgcggcuuuuugauucuucgaugucggcucuuccuagcaugg
ccaugcagccguggcgaaguguuggauuguucacccacuaacagggaacg
ugagcuggguuuagaccgucgugagacagguuaguuuuauccuacugucc
aaacaguugaagggaguguggauuaguacgaaaggaaacccacacgugac
cucuggugcagcgggugugcggaagugcaacugccaugcuacgucuccuc
aagcauagcuggaagccucuaagcuagaaaugaguccugacucuggaaga
cggccgggaagacgacccguaguuaacagcgguguuguacgauaugagcu
uucuauuguaguagcgaguauuugagacacugguuguuaccaccgucgu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p5d Spraguea lophii ribosome
• Resolution: 10.8 Å
• Binding residue (original residue number in PDB): S2 C3 N5 S7 H11 S13 A15 Y16 P18 K20 R21 K23 T25 K30 S31 K50 M53 R62 S64 K65 T66 Y97 L104 K105 I107 T109 R122 K125 R126 N127 S128 R129 S131 L133 M134 F135 L137 R162 P173 L177 K178 E184 T225 K226 G227 K228 G229 K230 K235 R236 T240 I241 H244 K245 S246 R247 K248 R251 K252 V253 A254 C255 I256 A258 W259 H260 A262 N263 V264 R265 R266 T267 R270 Q273 R278 R279 T280 M310 L314 R315 K320 I330 R341 F344 K351 K366 K367 G368 Y369 K378 F382
• Binding residue (residue number reindexed from 1): S1 C2 N4 S6 H10 S12 A14 Y15 P17 K19 R20 K22 T24 K29 S30 K49 M52 R61 S63 K64 T65 Y96 L103 K104 I106 T108 R121 K124 R125 N126 S127 R128 S130 L132 M133 F134 L136 R161 P172 L176 K177 E183 T224 K225 G226 K227 G228 K229 K234 R235 T239 I240 H243 K244 S245 R246 K247 R250 K251 V252 A253 C254 I255 A257 W258 H259 A261 N262 V263 R264 R265 T266 R269 Q272 R277 R278 T279 M309 L313 R314 K319 I329 R340 F343 K350 K365 K366 G367 Y368 K377 F381

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8p5d, PDBe:8p5d, PDBj:8p5d
• PDBsum: 8p5d
• PubMed: 37709902
• UniProt: S7XFB1