Structure of PDB 8azw Chain E Binding Site BS01

Receptor Information

>8azw Chain E (length=130) Species: 4097 (Nicotiana tabacum)

PFKRFVEIGRVALVNYGKDYGKLVVIVDVIDQNRALIDAPDMVRSQINFK
RLSLTDIKIDIKRIPKKKTLVAAMEAADVKNKWESSSWGRKLIVQKRRAS
LNDFDRFKLMLAKIKRAGVVRQELAKLKKE

Ligand information

>8azw Chain A (length=3196)

gcgaccccaggucaggcgggacuacccgcugaguuuaagcauaucaauaa
gcggaggaaaagaaacuuacaaggauuccccuaguaacggcgagcgaacc
gggaacagcccagccuuagaaucgggcggcuccgccguucgaauuguagu
cuggagaagcguccucagcggcggaccgggcccaaguccccuggaagggg
gcgccagagagggugagagccccguugugcccggacccugucgcaccacg
aggcgcugucuacgagucggguuguuugggaaugcagcccaaaucgggcg
gugaauuccguccaaggcuaaauacgggcgagagaccgauagcgaacaag
uaccgcgagggaaagaugaaaaggacuuugaaaagagagucaaagagugc
uugaaauugucgggagggaagcggaugggggccggcgaugcgccccgguc
ggauguggaacggugacgagccgguccgccgaucgacucggggcguggac
cagcguggauugggggggcggccaaagcccgggcuuucgauacgcccgug
gaacgccgucuccuugauugugguaggcagcgcgcgccuccggcgugcuu
cggcaucugcgcgcuccggacgcuggccugugggcuccccauucgacccg
ucuugaaacacggaccaaggagucugacaugugugcgagucaacgggcga
guaaacccguaaggcguaaggaagcugauuggugggaucccccugagggg
ugcaccgccgaccgaccuugaucuucugugaaggguucgagugugagcau
accugucgggacccgaaagauggugaacuaugccugagcggggcgaagcc
agaggaaacucugguggaggcccgcagcgauacugacgugcaaaucguuc
gucugacuuggguauaggggcgaaagacuaaucgaaccgucuaguagcug
guucccuccgaaguuucccucaggauagcuggagcucgcgugcgaguucu
aucggguaaagccaaugauuagaggcaucgggggcgcaacgcccucgacc
uauucucaaacuuuaaauagguaggacggugcggcugcuuuguugagccg
caccacggaaucaagagcuccaagugggccauuuuugguaagcagaacug
gcgaugcgggaugaaccggaagccggguuacggugccaaacugcgcgcua
accuagaucccacaaaggguguuggucgauuaagacagcgccgaaucaac
uagccccgaaaauggauggcgcuuaagcgcgcgaccuacacccggccguc
ggggcaagugccaggccccgaugaguaggagggcgcggcggucgcugcaa
aaccuugggcgcgagccugggcggagcggccgucggugcagaucuuggug
guaguagcaaauauucaaaugagaacuuugaaggccgaagaggggaaagg
uuccaugugaacggcacuugcacauggguuagucgauccuaagggucggg
ggaaccccgacagauagcgcguuucgcgcguacuccgaaagggaaucggg
uuaaaauuccugaaccgggacguggcgguugacggcaacguuaggaaguc
cggagacgucggcgggggccucgggaagaguuaucuuuucuguuuaacag
ccugcccacccuggaaacgacucagucggagguaggguccagcggcugga
agagcaccgcacgucgcgugguguccggugcgcccccggcggcccuugaa
aauccggaggaccgagugccguccacgcccggucguacucauaaccgcau
caggucuccaaggugaacagccucuggucgauggaacaauguaggcaagg
gaagucggcaaaauggauccguaacuucgggaaaaggauuggcucugagg
gcugggaacagccaacucagaacugguacggacaaggggaauccgacugu
uuaauuaaaacaaagcauugcgauggucccugcggauguuuacgcaaugu
gauuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcg
cggguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccu
cgucaucuaauuagugacgcgcaugaauggauuaacgagauucccacugu
cccugucuacuauccagcgaaaccacagccaagggaacgggcuuggcaga
aucagcggggaaagaagacccuguugagcuugacucuaguccgacuuugu
gaaaugacuugagaggguaguauaagugggagccggcgaaagugaaauac
cacuacuuuuaacguuauuuuacuuauuccgugaaucggaagcggggcac
ugccccucuuuuuggacccaaggcuugcuugcaggccgauccgggcggaa
gacauugucagguggggaguuuggcuggggcggcacaucuguuaaaagau
aacgcagguguccuaagaugagcucaacgagaacagaaaucucgugugga
acagaaggguaaaagcucguuugauucugauuuccaguacgaauacgaac
cgugaaagcguggccuaacgauccuuuagaccuucggaauucgaagcuag
aggugucagaaaaguuaccacagggauaacuggcuuguggcagccaagcg
uucauagcgacguugcuuuuugauccuucgaugucggcucuuccuaucau
ugugaagcagaauucaccaaguguuggauuguucacccaccaauagggaa
cgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacuga
ugacagugucgcaauaguaauucaaccuaguacgagaggaaccguugauu
cgcacaauuggucaucgcgcuugguugaaaagccaguggcgcgaagcuac
cgugcgcuggauuaugacugaacgccucuaagucagaauccgggcuagaa
gcgacgcaugcgcccgccguccgcuugccgacccgcaguaggggccuuug
gcccccaagggcacgugucguuggcuaagucaucguggcggaagagccgc
gguggccgccuugaaguacaauuuccaucgagcggcggguagaauccuuu
gcagacgacuuaaauacgcgacgggguauuguaaguggcagaguggccuu
gcugccacgauccacugagauucagcccuuugucgcuccgauucgu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<.......<.....>......
>>>>>..[[[....<......<<<<<<<<<...>>>>>>>>>......>.
....<<<<<<<<.<<<.<<<<<<<.<<<<<<.<<...<<<<......>>>
>.((......<<<.....))>>>..>>.>>>>>>...>>>>>>>.....>
>>>>>>>.>>>.......<<<<<<<........>>>>>>>.....(((((
..<<<<<<)))))..]]]................................
..<<....>>...............<<<<....>>>>.............
.....................<<<<<<<<<<<<......<<<<<<<<<<<
<...<<<<<.<<<<.....>>>>.>>>>>....>>>>.>>>>>>>>.<.<
<<<<<..<<<<<<<<<<<<<<<.....<<<<<<<.........>>>>>.>
>...>>>>>>>>>>>>>>>.........<<<<<<<<<<...>>>..<<..
..>>....>>>>>>>.....>>>>>>.>....>>>.>>>>>>>>>..<<<
<........>>>><<<<<<.....<<<<<.<<<<<<..<<<...<<<...
.....>>>....>>>...<<....>>....<<<<<...<<<<....>>>>
....>>>>>.<<<<<<<.....<....>.....>>.>>>.>>....>>>>
>>.>>>>>...<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<
<<<<....>>>>>>>.....>>>...<<<<.<<.<<........>>>>>>
>>....>>>>>>>>>...<<.......>>......>>>>>>...>..>.>
>..<<<<<<....<.<<<....>>>.><<<<<<<<<<......<<.<<<<
<<<.....<<<....<<<....<<<....<<<<<<.....>>>>>>..>>
>....>>>..>.>>.....>>>>>...<<<<<<<<<.<......>>>>>>
>>>>....>>>>..>>>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>
>>....<<<......>>>...<<<<<<<...<<<(((.....<<<<<<..
.....<..........<<<.<<<<<<.<<<.......<..>...>>>.>>
>>>>>>>..........))).>....>>>>>>.>>>...>>>>>>><<<<
<<<<<.........>>>>>>>>>....>>>>>><.<<<<<<<<<<.....
..<<<.<<<<....>>>>>>>....>>>>>>>>>>..>.....>>>>>><
<.....<<.....<<<<<<.......>>>>>><<<<.....<<<<<.<<.
..<<<<<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<
<....>>>........<<<<<...>>>>>.....>>....>>...<<<<<
........>>>>>))<<<<.<<<<<<<<...<<<....>>>...<...<<
<<<<...<<<<.<<<<<<<.<<<<<.<<<<.......>>>>.><...<<<
<<.....<<<<<<....<<<<...>>>>....>>>>>>.....>>>>>..
..><<<<<<<.......>>>>>>>>>>>...>>>>>>>.>>>>.......
..>>>>>>...>......>>>>.>>>>>>>>>>>>..>>.....<<....
..>>>>>>>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<
.........<.....<<<<<....<<..>>.....>>>>><<.<<<<<<<
<<<<....>>>>>..>>>>>>.>>............<<<<<<<<<..<<<
.........>>>..<<<<<<<....<<<<....>>>>......>>>>>>>
...<<..<<<..<<<<<<.<..<<<.....<<<<....>>>>.....>>>
>>>>>..>>>>><<<<<<.......>>>>>>........<..........
.<<<<<.......>>>>>.....>.....>>....>>.>>>>>>>..>..
>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>>....
[[[[[..{{{.{{......[[[[.{{[[[[..<<<<<.<<<.<<<...<<
<<<<<<<<.<<<<<<.........<<<<.<.<<<>>>............>
>>>>.>>>>>>..>>>>>>>>>>...<<<<<.....<<<<...<<<<<..
.>>>>>...............<<<<<<....>>>>>>..>>>>..>>>>>
......>>>.>>>..>>>>>...<<<.....>>>..<<<<<<........
...>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....
<<...(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.
<<<....>>>.>>))).......((((((..((((.>>>>>>))))))))
))..........]]]]..}}]]]].......<<.<.<.<<<<<<...<<.
......>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<<<
.<<<<<......>>>>>...>>>.<<<.........>>>.....>>>>>.
.>...>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]
]....<<<<<<<..<<<<.<.<<<<<.................>>>>>.>
<<<<<...<<<<....<<<<<<<<<......>>>>..>>>>>...>>>>.
.>>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>...
>>>>>>>....<<<<<<<<<.<<.<......<<.......<<<<<<...>
>>>>>....>>...........<<<...<<<<<<<<<<<......>>>>>
>>>>>>.>>>................>.>>.>>>>>>>>>.<<<<<.<..
...........>.....<<<<<<<<<.<<<....<<<<.<..<<<<<...
...>>>>>..>>>>>...>>>....>>>>..>>>>>...>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8azw Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution.
• Resolution: 2.14 Å
• Binding residue (original residue number in PDB): F3 K4 R5 Y17 D29 N34 N49 K51 R52 R64 S88 W89 Q96 R99 M111 L112 I115 R122 Q123 A126
• Binding residue (residue number reindexed from 1): F2 K3 R4 Y16 D28 N33 N48 K50 R51 R63 S87 W88 Q95 R98 M110 L111 I114 R121 Q122 A125

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

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

External links

• PDB: RCSB:8azw, PDBe:8azw, PDBj:8azw
• PDBsum: 8azw
• PubMed: 37156858
• UniProt: A0A1S4A807