Structure of PDB 8a3d Chain M Binding Site BS01

Receptor Information

>8a3d Chain M (length=176) Species: 9606 (Homo sapiens)

MKASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQ
LKKMKKSSGEIVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDL
TTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRPAVKQFHDSKI
KFPLPHRVLRRQHKPRFTTKRPNTFF

Ligand information

>8a3d Chain A (length=3303)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccggggggcccaaguccuucugaucgaggcccag
cccguggacggugugaggccgguagcggcccccggccgggucuucccgga
gucggguugcuugggaaugcagcccaaagcgggugguaaacuccaucuaa
ggcuaaauaccggcacgagaccgauagucaacaaguaccguaagggaaag
uugaaaagaacuuugaagagagaguucaagagggcgugaaaccguuaaga
gguaaacgggugggguccgcgcaguccgcccggaggauucaacccggcgg
cggguccggccgggcggaucugaccgucggcgaccggccgccgccgggcg
cauuuccaccgcggcggugcgccgcgaccggcuccgggacggcugggaag
gcccggcggggaagguggcucggccgaguguuacagcccccccggcagca
gcacucgccgaaucccggggccgagggaggucgccgcgcucuccccccug
ggggggccgggccaccccucccacggcgcgaccgcucggggcggacuguc
cccagugcgccccgggcgggucgcgccgucgggcccggggggccacgcgc
gcgucccgggacggcggagcgagcgcacggggucggcggcgacgucggcu
acccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgc
gagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggcc
ggccgaggugggaucccgaggccucucgccgagggcgcaccaccggcccg
ucucgcccgccgcgccggggagguggagcacgagcgcacguguuaggacc
cgaaagauggugaacuaugccugggcagggcgaagccagaggaaacucug
guggagguccguagcgguccugacgugcaaaucggucguccgaccugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaag
uuucccucaggauagcuggcgcucucggcaguuuuauccgguaaagcgaa
ugauuagagguaccuauucucaaacuuuaaauggguaagaagcccggcuc
gcuggcguggagccgggcguggaaugcgagugccuagugggccacuuuug
guaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcc
cgaugccgacgcucaucagaccccagaaaagguguugguugauauagaca
ggaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccauac
ccggccgucgccggcaguccgcggacgcuacgccgcgacgaguaggaggg
ccgcugcggugagccuugaagccuagggcgcgggcccggguggagccgcc
gcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuuga
aggccgaaguggagaaggguuccaugugaacagcaguugaacauggguca
gucgguccugagagaugggcgagcgccguuccgaagggggccgaucgaaa
gggagucggguucagauccccgaauccggagcggagaugggcgccgcgag
gcguccagugcgguaacgcgaccgaucccggagaagccggcgggagcccc
ggggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguu
cgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggc
guccggugagcucucgcuggcccuugaaaauccgggggagaggguguaaa
ucucgcgccgggccguacccauauccgcagcaggucuccaaggugaacag
ccucuggcauguuggaacaauguagguaagggaagucggcaagccggauc
cguaacuucgggauaaggauuggcucuaagggcuagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgggagcucucuu
aagguagccaaaugccucgucaucuaauuagugacgcgcaugaauggaug
aacgagauucccacugucccuaccuacuauccagcgaaaccacagccaag
ggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcuuga
cucuagucuggcacggugaagaguuuuucacugacccggugaggcggggg
gcgcuucuggcgccaagcgcccggccgggcgcgacccgcuccggggacag
ugccagguggggaguuugacuggggcgguacaccugucaaacgguaacgc
agguguccuaaggcgagcucagggaggacagaaaccucccguggagcaga
agggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccguga
aagcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggug
ucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguucau
agcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauuguga
agcagaauucaccaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaug
uguuguugccaugguaauccugcucaguacgagaggaaccgcagguucag
acauuugguguaugugcuuggcugaggagccaauggggcgaagcuaccau
cugugggauuaugacugaacgccucuaagucagaaucccgcccaggcgga
acgauacggcagcgccgcggagccucgguuggccucggauagccgguccc
cgggguccggugcggagugcccuucguccugggaaacggggcgcggccgg
aaaggcggccgcccccucgcccgucacgcaccgcacguucguggggaacc
uggcgcuaaaccauucguagacgaccugcuugggucgggguuucguacgu
agcagagcagcgcugcgaucuauugaaagucagcccucgacacaaggguu
ugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8a3d The chemical landscape of the human ribosome at 1.67 angstrom resolution.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): K2 A3 S4 G5 R8 Y63 Q66 V67 F68 K70 P72 S86 R87 S88 H91 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 A134 R139 F145 H146 D147 S148 P155 H156 R157 V158 R160 R161 H163 K164 P165 R166 T168 T169 K170 R171 P172 N173 T174 F175 F176
• Binding residue (residue number reindexed from 1): K2 A3 S4 G5 R8 Y63 Q66 V67 F68 K70 P72 S86 R87 S88 H91 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 A134 R139 F145 H146 D147 S148 P155 H156 R157 V158 R160 R161 H163 K164 P165 R166 T168 T169 K170 R171 P172 N173 T174 F175 F176

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8a3d, PDBe:8a3d, PDBj:8a3d
• PDBsum: 8a3d
• PubMed: 36909531
• UniProt: Q02543|RL18A_HUMAN Large ribosomal subunit protein eL20 (Gene Name=RPL18A)