Structure of PDB 5aj0 Chain AA Binding Site BS01

Receptor Information

>5aj0 Chain AA (length=252) Species: 9606 (Homo sapiens)

GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHD
PGRGAPLAKVVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNV
LPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVKLP
SGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRG
VAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKT
VQ

Ligand information

>5aj0 Chain A2 (length=3612)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgcgcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugucggcggcccggc
ggaucuuucccgcccccggggucggcgggggaccgucccccggaccggcg
accggccgccgccgggcgcauuuccaggcggugcgccgcgaccggcuccg
ggacggcugggaaggcccggcggggaagguggcucggggcccccgagugu
uacagcccccccggcagcagcacucgccgaaucccggggccgagggagcg
agacccgucgccgcgcucuccccccugggggggccgggccaccccuccca
cggcgcgaccgcucucccagggggcggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccggggggccacgcgcgcgucccgggac
ggcggagcgagcgcacggggucggcggcgacgucggcuacccacccgacc
cgucuugaaacacggaccaaggagucuaacacgugcgcgagucgggggcu
cgcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucgcc
ggccgaggugggaucccgaggccucuccaguccgccgaggggcaccaccg
gcccgucucgcccgccgcgccggggagguggagcacgagcgcacguguua
ggacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaa
cucugguggagguccguagcgguccugacgugcaaaucggucguccgacc
uggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuc
cgaaguuucccucaggauagcuggcgcucucgcccacgcaguuuuauccg
guaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauuc
ucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccggggu
ggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugc
gggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucaga
ccccagaaaagguguugguugauauagacagcaggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuag
cccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgcc
ggccuacgccgcgacgaguaggagggccgcugcggugagccuugaagccu
agggcgcgggcccggguggagccgccgcaggugcagaucuuggugguagu
agcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguucca
ugugaacagcaguugaacaugggucagucgguccugagagaugggcgagc
gccguuccgaagggacgggcgauggccuccguugcccucggccgaucgaa
agggagucggguucagauccccgaauccggaguggcggagaugggcgccg
cgaggcguccagugcgguaacgcgaccgaucccggagaagccggcgggag
ccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaaug
gguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccgg
cggcguccggugagcucucgcuggcccuugaaaauccgggggagagggug
uaaaucucgcgccgggccguacccauauccgcagcaggucuccaagguga
acagccucuggcauguuggaacaauguagguaagggaagucggcaagccg
gauccguaacuucgggauaaggauuggcucuaagggcuggcagccgacuu
agaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcau
cgcgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcu
cugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggag
uaacuaugacucucuuaagguagccaaaugccucgucaucuaauuaguga
cgcgcaugaauggaugaacgagauucccacugucccuaccuacuauccag
cgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaag
acccuguugagcuugacucuagucuggcacggugaagagacaugagaggu
guagaauaagugggaggcccgggccgccggugaaauaccacuacucugau
cguuuuuucacugacccggugaggcgggggggcgagcccgaggggcucuc
gcuucuggcgccaagcgcccgcccggccgggcgcgacccgcuccggggac
agugccagguggggaguuugacuggggcgguacaccugucaaacgguaac
gcagguguccuaaggcgagcucagggaggacagaaaccucccguggagca
gaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgu
gaaagcggggccucacgauccuucugaccuuuuggguuuuaagcaggagg
ugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguuc
auagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugu
gaagcagaauucgccaagcguuggauuguucacccacuaauagggaacgu
gagcuggguuuagaccgucgugagacagguuaguuuuacccuacugauga
uguguuguugccaugguaauccugcucaguacgagaggaaccgcagguuc
agacauuugguguaugugcuuggcugaggagccaauggggcgaagcuacc
aucugugggauuaugacugaacgccucuaagucagaaucccgcccaggcg
gaacgauacggcagcgccgcggagccucgguuggccucggauagccgguc
cgggguccggugcggagugcccuucguccugggaaacggggcgcggccgg
aaaggcggccgcccccucgcccgucacgcaccgcacguucguggggaacc
uggcgcuaaaccauucguagacgaccugcuucugggucgggguuucguac
guagcagagcagcucccucgcugcgaucuauugaaagucagcccucgaca
caaggguuuguc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5aj0 Structural Snapshots of Actively Translating Human Ribosomes
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): G2 R3 V4 R6 Q8 R9 K10 G11 S14 V15 R17 H19 V20 K21 H22 G25 A26 A31 F34 R37 Y40 K46 R54 R64 Y67 R68 F69 K70 K71 R72 F87 Y89 K93 Q95 E118 P120 G121 D122 R123 K125 L126 A127 R128 A129 S130 G131 N132 L150 S152 K156 G172 G173 R174 I175 P178 I179 L180 K181 A182 G183 A185 H187 K188 K192 R193 N194 C195 W196 P197 R198 V199 R200 G201 V202 A203 M204 N205 P206 V207 E208 H209 G213 G214 N215 H216 Q217 H218 G220 K221 P222 S223 T224 I225 R226 R227 A231 R233 K234 V235 G236 L237 I238 A239 A240 R241 R242 T243 G244 R245
• Binding residue (residue number reindexed from 1): G1 R2 V3 R5 Q7 R8 K9 G10 S13 V14 R16 H18 V19 K20 H21 G24 A25 A30 F33 R36 Y39 K45 R53 R63 Y66 R67 F68 K69 K70 R71 F86 Y88 K92 Q94 E117 P119 G120 D121 R122 K124 L125 A126 R127 A128 S129 G130 N131 L149 S151 K155 G171 G172 R173 I174 P177 I178 L179 K180 A181 G182 A184 H186 K187 K191 R192 N193 C194 W195 P196 R197 V198 R199 G200 V201 A202 M203 N204 P205 V206 E207 H208 G212 G213 N214 H215 Q216 H217 G219 K220 P221 S222 T223 I224 R225 R226 A230 R232 K233 V234 G235 L236 I237 A238 A239 R240 R241 T242 G243 R244

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0098794 postsynapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5aj0, PDBe:5aj0, PDBj:5aj0
• PDBsum: 5aj0
• PubMed: 25957688
• UniProt: P62917|RL8_HUMAN Large ribosomal subunit protein uL2 (Gene Name=RPL8)