Structure of PDB 7zjx Chain LG Binding Site BS01

Receptor Information

>7zjx Chain LG (length=294) Species: 9986 (Oryctolagus cuniculus)

cFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRM
IVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLA
RTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
QNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENP
VYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAA

Ligand information

>7zjx Chain L5 (length=3732)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcgguggggcgcgggaaau
guggcguacggaagacccacuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcgugguccggccgugccggcg
gucucggcggaucuuucccgcuccggggucggcgggggaccgccccccgg
ccggcgaccggccgccgccgggcgcauuuccaccgcggcggugcgccgcg
accggcuccgggacggcugggaaggccccggcggggaagguggcccgggg
ggacgccucgccggcgggcgcgaccccuccccggguguuacagccccgcc
ccggcagcagcagcucgccgaaucccggggccgagggagcgagaccugug
ucgccgcgcucuccccccucgggggggccgggccgccccucccacggcgc
gaccgcucggggcggacuguccccagugcgccccgggcgugucacgccgu
cgggcucgggggaggccacggcgcgucgcgcgccggcgcgcgcgcgcgag
cgagcgcacggggucggcggcgaugucggcuacccacccgacccgucuug
aaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacga
aagccgccguggcgcaaugaaggugaaggccggcggcggcgccgucgucg
gccgaggugggaucccgaggcccuuccaguccgccgagggcgcaccaccg
gcccgucucgcccgccgcgccggggagguggagcacgagcgcacguguua
ggacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaa
cucugguggagguccguagcgguccugacgugcaaaucggucguccgacc
uggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuc
cgaaguuucccucaggauagcuggcgcucucgcaaccccgcaguuuuauc
cgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuau
ucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccggg
cguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgc
ugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucauc
agaccccagaaaagguguugguugauauagacagcaggacgguggccaug
gaagucggaauccgcuaaggaguguguaacaacucaccugccgaaucaac
uagcccugaaaauggauggcgcuggagcgucgggcccauacccggccguc
gcuggcagucggcagagcgagaaagagaguggagccgcggacgcuacgcc
gcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcggg
cccggguggagccgccgcaggugcagaucuuggugguaguagcaaauauu
caaacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagc
aguugaacaugggucagucgguccugagagaugggcgagcgccguuccga
agggacgggcgauggccuccguugcccucagccgaucgaaagggagucgg
guucagauccccgaauccggaguggcggagaugggcgccgcgaggcgucc
agugcgguaacgcgaccgaucccggagaagccggcgggagccccggggag
aguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcccc
gagagaggggcccgugccuuggaaagcgucgcgguuccggcggcguccgg
ugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgc
gccgggccguacccauauccgcagcaggucuccaaggugaacagccucug
gcauguuggaacaauguagguaagggaagucggcaagccggauccguaac
uucgggauaaggauuggcucuaagggcugguagcagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuau
gacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcau
gaauggaugaacgagauucccacugucccuaccuacuauccagcgaaacc
acagccaagggaacgggcuuggcggaaucagcggggaaagaagacccugu
ugagcuugacucuagucuggcacggugaagagacaugagagguguagaau
aagugggaggcccgggccgccggugaaauaccacuacucuuaucguuuuu
ucacugacccggugaggcgggggggcgagccccgaggggcucucgcuucu
ggcgccaagcgccgggccccgucgguccgggccggcggcggccgggcgcg
acccgcuccggggacagugccagguggggaguuugacuggggcgguacac
cugucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaa
accucccguggagcagaagggcaaaagcucgcuugaucuugauuuucagu
acgaauacagaccgugaaagcggggccucacgauccuucugagcuuuugg
guuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugu
ggcggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggc
ucuuccuaucauugugaagcagaauucaccaagcguuggauuguucaccc
acuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguu
uuacccuacugaugauguguuguugccaugguaauccugcucaguacgag
aggaaccgcagguucagacauuugguguaugugcuuggcugaggagccaa
uggggcgaagcuaccaucugugggauuaugacugaacgccucuaagucag
aaucccgcccaggcggaacgauacggcagcgccgaaggagccucgguugg
ccucggauagccggucccccgcgggguccggugcggagagcccuucgucc
cgggaaauggggcgcggccggaaagggggccgcccucucgcccgucacgc
accgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugc
uucugggucgggguuucguacguagcagagcagcucccucgcugcgaucu
auugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7zjx Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): X2 F3 V4 K5 K8 Y12 K14 R15 Y16 Q17 K19 R23 G26 T28 D29 Y31 R35 L36 K43 Y44 K48 Y49 F113 M115 P139 G140 Y145 L146 L150 R152 T153 F160 P174 H175 S176 K178 R179 S272 A274 Q275 D278 R279 Q282 K283 S286 R289
• Binding residue (residue number reindexed from 1): X1 F2 V3 K4 K7 Y11 K13 R14 Y15 Q16 K18 R22 G25 T27 D28 Y30 R34 L35 K42 Y43 K47 Y48 F112 M114 P138 G139 Y144 L145 L149 R151 T152 F159 P173 H174 S175 K177 R178 S271 A273 Q274 D277 R278 Q281 K282 S285 R288

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7zjx, PDBe:7zjx, PDBj:7zjx
• PDBsum: 7zjx
• PubMed: 35709277
• UniProt: P19949|RL5_RABIT Large ribosomal subunit protein uL18 (Gene Name=RPL5)