Structure of PDB 6y0g Chain LR Binding Site BS01

Receptor Information

>6y0g Chain LR (length=180) Species: 9606 (Homo sapiens)

SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLII
RKPVTVHSRARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRI
LRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIHKLKADKAR
KKLLADQAEARRSKTKEARKRREERLQAKK

Ligand information

>6y0g Chain L5 (length=3644)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcggggggggccgggccaccc
cucccacggcgcgaccgcucggggcggacuguccccagugcgccccgggc
gggucgcgccgucgggcccgggggaggccacgcgcgcgucccccgagggg
gacggcggagcgagcgcacggggucggcggcgacgucggcuacccacccg
acccgucuugaaacacggaccaaggagucuaacacgugcgcgagucgggg
gcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcuc
gccggccgaggugggaucccgaggccucuccaguccgccgagggcgcacc
accggcccgucucgcccgccgcgccggggagguggagcacgagcgcacgu
guuaggacccgaaagauggugaacuaugccugggcagggcgaagccagag
gaaacucugguggagguccguagcgguccugacgugcaaaucggucgucc
gaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuc
ccuccgaaguuucccucaggauagcuggcgcucucgcagacccgacccgc
cacgcaguuuuauccgguaaagcgaaugauuagaggucuuggggccgaaa
gaucucaaccuauucucaaacuuuaaauggguaagaagcccggcucgcug
gcguggagccgggcguggaaugcgagugccuagugggccacuuuugguaa
gcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgau
gccgacgcucaucagaccccagaaaagguguugguugauauagacagcag
gacgguggcaagucgcuaaggagguguaacaacucaccugccgaaucaac
uagcccugaaaauggauggcgcuggagcgucgggcccauacccggccguc
gccggcagucgagaguggacgggagcgggcggcgcgccgcgcccggagcc
ccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagccuug
aagccuagggcgcgggcccggguggagccgccgcaggugcagaucuuggu
gguaguagcaaauauucaaacgagaacuuugaaggccgaaguggagaagg
guuccaugugaacagcaguugaacaugggucagucgguccugagagaugg
gcgagcgccguuccgaagggacgggcgauggccuccguugcccucggccg
aucgaaagggagucggguucagauccccgaauccggaguggcggagaugg
gcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaagccgg
cgggagccccggggagaguucucuuuucuuugugaagggcagggcgcccu
ggaauggguucgccccgagagaggggcccgugccuuggaaagcgucgcgg
uuccggcggcguccggugagcucucgcuggcccuugaaaauccgggggag
aggguguaaaucucgcgccgggccguacccauauccgcagcaggucucca
aggugaacagccucuggcauguuggaacaauguagguaagggaagucggc
aagccggauccguaacuucgggauaaggauuggcucuaagggcugggucg
gucgcggccggcgccuagcagccgacuuagaacuggugcggaccagggga
auccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgggugu
ugacgcgaugugauuucugcccagugcucugaaugucaaagugaagaaau
ucaaugaagcgcggguaaacggcgggaguaacuaugacucucuuaaggua
gccaaaugccucgucaucuaauuagugacgcgcaugaauggaugaacgag
auucccacugucccuaccuacuauccagcgaaaccacagccaagggaacg
ggcuuggcggaaucagcggggaaagaagacccuguugagcuugacucuag
ucuggcacggugaagagacaguuuuuucacugacccggugaggcgggggg
gcgagccccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgc
cggccgggcgcgacccgcuccggggacagugccagguggggaguuugacu
ggggcgguacaccugucaaacgguaacgcagguguccuaaggcgagcuca
gggaggacagaaaccucccguggagcagaagggcaaaagcucgcuugauc
uugauuuucaguacgaauacagaccgugaaagcggggccucacgauccuu
cugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacaggga
uaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuugaucc
uucgaugucggcucuuccuaucauugugaagcagaauucaccaagcguug
gauuguucacccacuaauagggaacgugagcuggguuuagaccgucguga
gacagguuaguuuuacccuacugaugauguguuguugccaugguaauccu
gcucaguacgagaggaaccgcagguucagacauuugguguaugugcuugg
cugaggagccaauggggcgaagcuaccaucugugggauuaugacugaacg
ccucuaagucagaaucccgcccaggcggaacgauacggcagcgccgcgga
gccucgguuggccucggauagccggucccccgccgggguccggugcggag
ugcccuucguccugggaaacggggcgcggccggagaggcggccgcccccu
cgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucg
uagacgaccugcuucugggucgggguuucguacguagcagagcagcuccc
ucgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6y0g Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): L4 R5 K8 R9 G18 K19 K20 K21 W23 L24 P26 S37 R38 Q39 Q40 K43 K46 V55 T56 V57 H58 S59 R60 A61 R62 R64 R70 R71 R74 H75 M76 G77 I78 G79 K80 R81 K82 G83 T84 N86 A87 R88 M89 K92 V93 W95 M96 R100 R103 R108 R110 K114 R117 H118 Y120 H121 Y124 L125 K126 K128 G129 N130 N134 K135 H143 K146
• Binding residue (residue number reindexed from 1): L3 R4 K7 R8 G17 K18 K19 K20 W22 L23 P25 S36 R37 Q38 Q39 K42 K45 V54 T55 V56 H57 S58 R59 A60 R61 R63 R69 R70 R73 H74 M75 G76 I77 G78 K79 R80 K81 G82 T83 N85 A86 R87 M88 K91 V92 W94 M95 R99 R102 R107 R109 K113 R116 H117 Y119 H120 Y123 L124 K125 K127 G128 N129 N133 K134 H142 K145

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:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6y0g, PDBe:6y0g, PDBj:6y0g
• PDBsum: 6y0g
• PubMed: 32268098
• UniProt: P84098|RL19_HUMAN Large ribosomal subunit protein eL19 (Gene Name=RPL19)