Structure of PDB 7bhp Chain LN Binding Site BS01

Receptor Information

>7bhp Chain LN (length=203) Species: 9606 (Homo sapiens)

GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRL
GYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSV
AEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWI
TKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLH
RYR

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 Y4 Q8 R12 K14 Q15 R24 W28 R31 P40 R41 R44 K47 R49 R50 L51 K54 A55 K56 Q57 R65 R67 R68 G69 G70 R71 K72 R73 P74 V75 K77 Y81 G82 K83 P84 V85 H86 H87 V89 N90 Q91 K93 F94 A95 R96 S97 L98 R105 R108 A112 E123 S125 F138 K140 A141 R144 W150 H156 K157 M161 R162 S166 R169 K170 S171 R172 K176 G177 H178 K179 F180 H181 H182 I184 G186 S187 R188 R189 W192 R193 R194 R195 Q199 H201 R202 R204
• Binding residue (residue number reindexed from 1): G1 Y3 Q7 R11 K13 Q14 R23 W27 R30 P39 R40 R43 K46 R48 R49 L50 K53 A54 K55 Q56 R64 R66 R67 G68 G69 R70 K71 R72 P73 V74 K76 Y80 G81 K82 P83 V84 H85 H86 V88 N89 Q90 K92 F93 A94 R95 S96 L97 R104 R107 A111 E122 S124 F137 K139 A140 R143 W149 H155 K156 M160 R161 S165 R168 K169 S170 R171 K175 G176 H177 K178 F179 H180 H181 I183 G185 S186 R187 R188 W191 R192 R193 R194 Q198 H200 R201 R203

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:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0045471 response to ethanol

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0031672 A band
• GO:0044391 ribosomal subunit
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7bhp, PDBe:7bhp, PDBj:7bhp
• PDBsum: 7bhp
• PubMed: 33479117
• UniProt: P61313|RL15_HUMAN Large ribosomal subunit protein eL15 (Gene Name=RPL15)