Structure of PDB 7bhp Chain LD Binding Site BS01

Receptor Information

>7bhp Chain LD (length=290) Species: 9606 (Homo sapiens)

GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRM
IVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLA
RTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
QNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENP
VYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQ

Ligand information

>7bhp 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

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7bhp Dynamic association of human Ebp1 with the ribosome.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): G2 F3 K5 K10 A11 Y12 R15 Y16 Q17 K19 R23 T28 D29 Y31 R35 L36 K43 Y44 K48 F113 P139 G140 F142 Y145 L146 A148 L150 T153 F160 H175 S176 R179 Q275 D278 R279 Q282 S286 R289 A290
• Binding residue (residue number reindexed from 1): G1 F2 K4 K9 A10 Y11 R14 Y15 Q16 K18 R22 T27 D28 Y30 R34 L35 K42 Y43 K47 F112 P138 G139 F141 Y144 L145 A147 L149 T152 F159 H174 S175 R178 Q274 D277 R278 Q281 S285 R288 A289

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003730 mRNA 3'-UTR binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0031625 ubiquitin protein ligase binding
• GO:0048027 mRNA 5'-UTR binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0010628 positive regulation of gene expression
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
• GO:2000435 negative regulation of protein neddylation

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7bhp, PDBe:7bhp, PDBj:7bhp
• PDBsum: 7bhp
• PubMed: 33479117
• UniProt: P46777|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)