Structure of PDB 6y57 Chain Lc Binding Site BS01

Receptor Information

>6y57 Chain Lc (length=93) Species: 9606 (Homo sapiens)

INSRLQLVMKSGKYVLGYKQTLKMIRQGKAKLVILANNCPALRKSEIEYY
AMLAKTGVHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIR

Ligand information

>6y57 Chain L5 (length=3574)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccgggggggccgggccaccccucc
cacggcgcgaccgcucggggcggacuguccccagugcgccccgggcgggu
cgcgccgucgggcccgggggaggccacgcgcgcgucccccgagggggacg
gcggagcgagcgcacggggucggcggcgacgucggcuacccacccgaccc
gucuugaaacacggaccaaggagucuaacacgugcgcgagucgggggcuc
gcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucgccg
gccgaggugggaucccgaggccucuccaguccgccgagggcgcaccaccg
gcccgucucgcccgccgcgccggggagguggagcacgagcgcacguguua
ggacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaa
cucugguggagguccguagcgguccugacgugcaaaucggucguccgacc
uggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuc
cgaaguuucccucaggauagcuggcgcucucgcagacccgaccgccacgc
aguuuuauccgguaaagcgaaugauuagaggucuuggggcucucaaccua
uucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgg
gcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcg
cugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucau
cagaccccagaaaagguguugguugauauagacagcaggacccgcuaagc
accugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggc
ccauacccggccgucgccggcagucgagaguggacgggagcgcggcgcgc
gccccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagcc
uugaagccuagggcgcgggcccggguggagccgccgcaggugcagaucuu
ggugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggaga
aggguuccaugugaacagcaguugaacaugggucagucgguccugagaga
ugggcgagcgccguuccgaagggacgggcgaccguugcccucggccgauc
gaaagggagucggguucagauccccgaauccggaguggcggagaugggcg
ccgcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcgg
gagccccggggagaguucucuuuucuuugugaagggcagggcgcccugga
auggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuc
cggcggcguccggugagcucucgcuggcccuugaaaauccgggggagagg
guguaaaucucgcgccgggccguacccauauccgcagcaggucuccaagg
ugaacagccucuggcauguuggaacaauguagguaagggaagucggcaag
ccggauccguaacuucgggauaaggauuggcucuaagggcuggguccggc
cggcgccuagcagccgacuuagaacuggugcggaccaggggaauccgacu
guuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcga
ugugauuucugcccagugcucugaaugucaaagugaagaaauucaaugaa
gcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaaug
ccucgucaucuaauuagugacgcgcaugaauggaugaacgagauucccac
ugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuuggc
ggaaucagcggggaaagaagacccuguugagcuugacucuagucuggcac
ggugaagagauuuuucacugacccggugaggcgggggggcgagccgggcu
cucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccg
cuccggggacagugccagguggggaguuugacuggggcgguacaccuguc
aaacgguaacgcagguguccuaaggcgagcucagggaggacagaaaccuc
ccguggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaa
uacagaccgugaaagcggggccucacgauccuucugaccuuuuggguuuu
aagcaggaggugucagaaaaguuaccacagggauaacuggcuuguggcgg
ccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuc
cuaucauugugaagcagaauucaccaagcguuggauuguucacccacuaa
uagggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacc
cuacugaugauguguuguugccaugguaauccugcucaguacgagaggaa
ccgcagguucagacauuugguguaugugcuuggcugaggagccaaugggg
cgaagcuaccaucugugggauuaugacugaacgccucuaagucagaaucc
cgcccaggcggaacgauacggcagcgccgcggagccucgguuggccucgg
auagccggucccccgccgggguccggugcggagugcccuucguccuggga
aacggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgc
acguucguggggaaccuggcgcuaaaccauucguagacgaccugcuucug
ggucgggguuucguacguagcagagcagcuucgcugcgaucuauugaaag
ucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6y57 Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): L29 G30 Y31 Q33 K36 N51 A54 S58 Y88 Y89 R90 C92
• Binding residue (residue number reindexed from 1): L16 G17 Y18 Q20 K23 N38 A41 S45 Y75 Y76 R77 C79

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
• GO:0031640 killing of cells of another organism
• GO:0050829 defense response to Gram-negative bacterium
• GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6y57, PDBe:6y57, PDBj:6y57
• PDBsum: 6y57
• PubMed: 32268098
• UniProt: P62888|RL30_HUMAN Large ribosomal subunit protein eL30 (Gene Name=RPL30)