Structure of PDB 6y2l Chain LI Binding Site BS01

Receptor Information

>6y2l Chain LI (length=206) Species: 9606 (Homo sapiens)

GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLGGH
MVSDEYEQLSSEALEAARICANKYMVKSCGRDGFHMRVRLHPFHVIRINK
MLLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNEEHVIEALRRAKFK
FPGRQKIHISKKWGFTKFNADEFEDMVAKKCLIPDGCGVKYVPSHGPLDK
WRVLHS

Ligand information

>6y2l Chain L5 (length=3613)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcgguccggccgugucggcggc
ccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggcc
gccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggga
cggcugggaaggcccggcggggaagguggcucgggggcccccgaguguua
cagcccccccggcagcagcacucgccgaaucccggggccgagggagcgag
acccgucgccgcgcucuccccccucccggggggggccgggccaccccucc
cacggcgcgaccgcucggggcggacuguccccagugcgccccgggcgggu
cgcgccgucgggcccgggggggccacgcgcgcgucccccgagggggacgg
cggagcgagcgcacggggucggcggcgacgucggcuacccacccgacccg
ucuugaaacacggaccaaggagucuaacacgugcgcgagucgggggcucg
cacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucgccgg
ccgaggugggaucccgaggccucuccaguccgccgagggcgcaccaccgg
cccgucucgcccgccgcgccggggagguggagcacgagcgcacguguuag
gacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaac
ucugguggagguccguagcgguccugacgugcaaaucggucguccgaccu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccucc
gaaguuucccucaggauagcuggcgcucucgcagacccgaccgccacgca
guuuuauccgguaaagcgaaugauuagaggucuuggggccgaaagaucuc
aaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcgugg
agccgggcguggaaugcgagugccuagugggccacuuuugguaagcagaa
cuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgac
gcucaucagaccccagaaaagguguugguugauauagacagcaggacggu
ggcgcuaaccugccgaaucaacuagcccugaaaauggauggcgcuggagc
gucgggcccauacccggccgucgccggcagucgagaguggacgggagcgg
cggcgcgcccggagccccgcggacgcuacgccgcgacgaguaggagggcc
gcugcggugagccuugaagccuagggcgcgggcccggguggagccgccgc
aggugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaag
gccgaaguggagaaggguuccaugugaacagcaguugaacaugggucagu
cgguccugagagaugggcgagcgccguuccgaagggacgggcgauggccu
ccguugcccucggccgaucgaaagggagucggguucagauccccgaaucc
ggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccg
aucccggagaagccggcgggagccccggggagaguucucuuuucuuugug
aagggcagggcgcccuggaauggguucgccccgagagaggggcccgugcc
uuggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccu
ugaaaauccgggggagaggguguaaaucucgcgccgggccguacccauau
ccgcagcaggucuccaaggugaacagccucuggcauguuggaacaaugua
gguaagggaagucggcaagccggauccguaacuucgggauaaggauuggc
ucuaagggcugggucggucgcggccggcgccuagcagccgacuuagaacu
ggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaa
ggcccgcggcggguguugacgcgaugugauuucugcccagugcucugaau
gucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacua
ugacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgca
ugaauggaugaacgagauucccacugucccuaccuacuauccagcgaaac
cacagccaagggaacgggcuuggcggaaucagcggggaaagaagacccug
uugagcuugacucuagucuggcacggugaagagacaaucguuuuuucacu
gacccggugaggcgggggggcgagccccgaggggcucucgcuucuggcgc
caagcgcccggccgcgcgccggccgggcgcgacccgcuccggggacagug
ccagguggggaguuugacuggggcgguacaccugucaaacgguaacgcag
guguccuaaggcgagcucagggaggacagaaaccucccguggagcagaag
ggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgugaaa
gcggggccucacgauccuucugaccuuuuggguuuuaagcaggagguguc
agaaaaguuaccacagggauaacuggcuuguggcggccaagcguucauag
cgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugugaag
cagaauucaccaagcguuggauuguucacccacuaauagggaacgugagc
uggguuuagaccgucgugagacagguuaguuuuacccuacugaugaugug
uuguugccaugguaauccugcucaguacgagaggaaccgcagguucagac
auuugguguaugugcuuggcugaggagccaauggggcgaagcuaccaucu
gugggauuaugacugaacgccucuaagucagaaucccgcccaggcggaac
gauacggcagcgccgcggagccucgguuggccucggauagccgguccccc
gccgggguccggugcggagugcccuucguccugggaaacggggcgcggcc
ggagaggcggccgcccccucgcccgucacgcaccgcacguucguggggaa
ccuggcgcuaaaccauucguagacgaccugcuucugggucgggguuucgu
acguagcagagcagcucccucgcugcgaucuauugaaagucagcccucga
cacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6y2l Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): R3 R4 P5 A6 R7 K13 N14 K15 Y17 F22 D35 K39 S61 E63 A67 K74 R88 R90 H92 F94 R98 N100 Q112 M115 R116 G117 A118 F119 G120 Q133 F157 K158 P160 G194 K198
• Binding residue (residue number reindexed from 1): R2 R3 P4 A5 R6 K12 N13 K14 Y16 F21 D34 K38 S60 E62 A66 K73 R87 R89 H91 F93 R97 N99 Q104 M107 R108 G109 A110 F111 G112 Q125 F149 K150 P152 G186 K190

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation
• GO:0007141 male meiosis I
• GO:0007283 spermatogenesis
• GO:0030154 cell differentiation
• GO:0051321 meiotic cell cycle

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6y2l, PDBe:6y2l, PDBj:6y2l
• PDBsum: 6y2l
• PubMed: 32268098
• UniProt: Q96L21|RL10L_HUMAN Ribosomal protein uL16-like (Gene Name=RPL10L)