Structure of PDB 8a3d Chain Y Binding Site BS01

Receptor Information

>8a3d Chain Y (length=128) Species: 9606 (Homo sapiens)

AALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKG
QILMPNIGYGSNKKTKHMLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAH
NVSSKNRKAIVERAAQLAIRVTNPNARL

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): R5 L7 V8 K14 K15 R16 T17 K18 K19 F20 R22 H23 Q24 D26 R27 Y28 V29 K30 I31 N34 W35 R36 K37 R39 G40 I41 D42 N43 R44 R46 R47 R48 F49 K50 G51 Q52 P56 N57 I58 G59 Y60 G61 S62 N63 K64 K65 K67 H68 K76 N81 K83 E98 A100 H101 N102 S104 S105 K106 N107 R108 N124 N126 A127 R128
• Binding residue (residue number reindexed from 1): R4 L6 V7 K13 K14 R15 T16 K17 K18 F19 R21 H22 Q23 D25 R26 Y27 V28 K29 I30 N33 W34 R35 K36 R38 G39 I40 D41 N42 R43 R45 R46 R47 F48 K49 G50 Q51 P55 N56 I57 G58 Y59 G60 S61 N62 K63 K64 K66 H67 K75 N80 K82 E97 A99 H100 N101 S103 S104 K105 N106 R107 N123 N125 A126 R127

Gene Ontology

Molecular Function

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

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: P62910|RL32_HUMAN Large ribosomal subunit protein eL32 (Gene Name=RPL32)