Structure of PDB 8g60 Chain Lj Binding Site BS02

Receptor Information

>8g60 Chain Lj (length=86) Species: 9606 (Homo sapiens)

TKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSA
KAKRRNTTGTGRMRHLKIVYRRFRHGFREGTTPKPK

Ligand information

>8g60 Chain L5 (length=3637)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggggggaccgucccccgaccggcgaccggccgccgc
cgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggcu
gggaaggcccggcggggaagguggcucgggggcccccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccugggggggccgggccaccccucccacggcgcg
accgcucgggcggacuguccccagugcgccccgggcgggucgcgccgucg
ggcccggggggccacgcgcgcguccccggggacggcggagcgagcgcacg
gggucggcggcgacgucggcuacccacccgacccgucuugaaacacggac
caaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccgu
ggcgcaaugaaggugaaggccggcgcgcucgccggccgaggugggauccc
gaggccucuccaguccgccgagggcgcaccaccggcccgucucgcccgcc
gcgccggggagguggagcacgagcgcacguguuaggacccgaaagauggu
gaacuaugccugggcagggcgaagccagaggaaacucugguggagguccg
uagcgguccugacgugcaaaucggucguccgaccuggguauaggggcgaa
agacuaaucgaaccaucuaguagcugguucccuccgaaguuucccucagg
auagcuggcgcucucgcagacccgaacgcaguuuuauccgguaaagcgaa
ugauuagaggucuuggggccgaaacgaucucaaccuauucucaaacuuua
aauggguaagaagcccggcucgcuggcguggagccgggcguggaaugcga
gugccuagugggccacuuuugguaagcagaacuggcgcugcgggaugaac
cgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccagaaa
agguguugguugauauagacagcaggacgguggccauggaagucggaauc
cgcuaaggaguguguaacaacucaccugccgaaucaacuagcccugaaaa
uggauggcgcuggagcgucgggcccauacccggccgucgccggcagucga
gaguggacgggagcgcgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
agcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauccc
ggagaagccggcgggagccccggggagaguucucuuuucuuugugaaggg
cagggcgcccuggaauggguucgccccgagagaggggcccgugccuugga
aagcgucgcgguuccggcggcguccggugagcucucgcuggcccuugaaa
auccgggggagaggguguaaaucucgcgccgggccguacccauauccgca
gcaggucuccaaggugaacagccucuggcauguuggaacaauguagguaa
gggaagucggcaagccggauccguaacuucgggauaaggauuggcucuaa
gggcuggguagcagccgacuuagaacuggugcggaccaggggaauccgac
uguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcg
augugauuucugcccagugcucugaaugucaaagugaagaaauucaauga
agcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaau
gccucgucaucuaauuagugacgcgcaugaauggaugaacgagauuccca
cugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuugg
cggaaucagcggggaaagaagacccuguugagcuugacucuagucuggca
cggugaagagacaugagagguguagaauaagugggaggcccgggccgccg
gugaaauaccacuacucugaucguuuuuucacugacccggugaggcgggg
gggcgagccccgaggggcucucgcuucuggcgccaagcgcccggcgccgg
gcgcgacccgcuccggggacagugccagguggggaguuugacuggggcgg
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacugg
cuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgaug
ucggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguu
cacccacuaauagggaacgugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugauguguuguugccaugguaauccugcucagu
acgagaggaaccgcagguucagacauuugguguaugugcuuggcugagga
gccaauggggcgaagcuaccaucugugggauuaugacugaacgccucuaa
gucagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgg
uuggccucggauagccggucccccgccgggguccggugcggagugcccuu
cguccugggaaacggggcgcggccggagaggcggccgcccccucgcccgu
cacgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacga
ccugcuucugggucgggguuucguacguagcagagcagcucccucgcugc
gaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g60 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.54 Å
• Binding residue (original residue number in PDB): T2 K3 G4 T5 S6 S7 F8 G9 K10 R11 R12 N13 K14 T15 H16 K25 A26 H28 Q30 K31 G35 K36 R43 K44 R45 K46 Y47 N48 W49 K52 A53 R55 R56 T58 T59 Y71 R75 K85
• Binding residue (residue number reindexed from 1): T1 K2 G3 T4 S5 S6 F7 G8 K9 R10 R11 N12 K13 T14 H15 K24 A25 H27 Q29 K30 G34 K35 R42 K43 R44 K45 Y46 N47 W48 K51 A52 R54 R55 T57 T58 Y70 R74 K84

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding
• GO:0097371 MDM2/MDM4 family protein binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:1901798 positive regulation of signal transduction by p53 class mediator

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g60, PDBe:8g60, PDBj:8g60
• PDBsum: 8g60
• PubMed: 37020024
• UniProt: P61927|RL37_HUMAN Large ribosomal subunit protein eL37 (Gene Name=RPL37)