Structure of PDB 4ug0 Chain LG Binding Site BS01

Receptor Information

>4ug0 Chain LG (length=241) Species: 9606 (Homo sapiens)

KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLK
VPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGK
GDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCR
KMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTN
YNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG

Ligand information

>4ug0 Chain L5 (length=3776)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucggccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccucccggcgccgccggggggggccgggccaccc
cucccacggcgcgaccgcucggggcggacuguccccagugcgccccgggc
gggucgcgccgucgggcccgggggaggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacgugcaaaucggu
cguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcu
gguucccuccgaaguuucccucaggauagcuggcgcucucgcacacgcag
uuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucuc
aaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcguga
gccgggcguggaauggagugccuagugggccacuuuugguaagcagaacu
ggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgc
ucaucagaccccagaaaagguguugguugauauagacagcaggacggugg
ccauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgccggcagucgagaguggacgggagcggcgggggcggcgcgcgcg
cgcgcccgcccccggagccccgcggacgcuacgccgcgacgaguaggagg
gccgcugcggugagccuugaagccuagggcgcgggcccggguggagccgc
cgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuug
aaggccgaaguggagaaggguuccaugugaacagcaguugaacauggguc
agucgguccugagagaugggcgagcgccguuccgaagggacgggcgaugg
ccuccguugcccucggccgaucgaaagggagucggguucagauccccgaa
uccggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcga
ccgaucccggagaagccggcgggagccccggggagaguucucuuuucuuu
gugaagggcagggcgcccuggaauggguucgccccgagagaggggcccgu
gccuuggaaagcgucgcgguuccggcggcguccggugagcucucgcuggc
ccuugaaaauccgggggagaggguguaaaucucgcgccgggccguaccca
uauccgcagcaggucuccaaggugaacagccucuggcauguuggaacaau
guagguaagggaagucggcaagccggauccguaacuucgggauaaggauu
ggcucuaagggcugggucggucgucggccggcgccuagcagccgacuuag
aacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucg
cgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcucu
gaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggagua
acuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacg
cgcaugaauggaugaacgagauucccacugucccuaccuacuauccagcg
aaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaagac
ccuguugagcuugacucuagucuggcacggugaagagacaugagaggugu
agaauaagugggaggcccccggcgcccccccgguguccccgcgaggggcc
cggggcgggguccgccggcccugcgggccgccggugaaauaccacuacuc
ugaucguuuuuucacugacccggugaggcgggggggcgagccccgagggg
cucucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacc
cgcuccggggacagugccagguggggaguuugacuggggcgguacaccug
ucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaaacc
ucccguggagcagaagggcaaaagcucgcuugaucuugauuuucaguacg
aauacagaccgugaaagcggggccucacgauccuucugaccuuuuggguu
uuaagcaggaggugucagaaaaguuaccacagggauaacuggcuuguggc
ggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcucu
uccuaucauugugaagcagaauucaccaagcguuggauuguucacccacu
aauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuua
cccuacugaugauguguuguugccaugguaauccugcucaguacgagagg
aaccgcagguucagacauuugguguaugugcuuggcugaggagccaaugg
ggcgaagcuaccaucugugggauuaugacugaacgccucuaagucagaau
cccgcccaggcggaacgauacggcagcgccgcggagccucgguuggccuc
ggauagccggucccccgcgggguccggugcggagugcccuucguccuggg
aaacggggcgcggccggagaggcggccgcccccucgcccgucacgcacgc
cguucguggggaaccuggcgcuaaaccauucguagacgaccugcuucugg
gucgggguuucguacguagcagagcagcucccucgcugcgaucuauugaa
agucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ug0 Structure of the human 80S ribosome
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): K34 R35 K37 F39 I41 Q43 I45 Q46 K48 R49 R53 F54 K56 R59 Y60 I69 L70 R73 E105 K110 R113 R132 G139 V140 N141 T142 V161 D162 P163 A188 R196 K197 T200 V241 K245 R249
• Binding residue (residue number reindexed from 1): K9 R10 K12 F14 I16 Q18 I20 Q21 K23 R24 R28 F29 K31 R34 Y35 I44 L45 R48 E80 K85 R88 R107 G114 V115 N116 T117 V136 D137 P138 A163 R171 K172 T175 V216 K220 R224

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• 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:4ug0, PDBe:4ug0, PDBj:4ug0
• PDBsum: 4ug0
• PubMed: 25901680
• UniProt: P62424|RL7A_HUMAN Large ribosomal subunit protein eL8 (Gene Name=RPL7A)