Structure of PDB 8glp Chain LO Binding Site BS01

Receptor Information

>8glp Chain LO (length=202) Species: 9606 (Homo sapiens)

AEVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNK
LKYLAFLRKRMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDR
LKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVGWKYQA
VTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGL
LV

Ligand information

>8glp Chain L5 (length=3546)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggcgggggaccgucccccgaccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggcccggcggggaagguggcucgggggcccccgaguguuacag
cccccccggcagcagcacucgccgaaucccggggccgagggagcgagacc
cgucgccgcgcucuccccccugggggggccgggccaccccucccacggcg
cgaccgcucggggcggacuguccccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgcgcgucccccgaagagggggacggcggag
cgagcgcacggggucggcggcgacgucggcuacccacccgacccgucuug
aaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacga
aagccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgag
gugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgu
cucgcccgccgcgccggggagguggagcacgagcgcacguguuaggaccc
gaaagauggugaacuaugccugggcagggcgaagccagaggaaacucugg
uggagguccguagcgguccugacgugcaaaucggucguccgaccugggua
uaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaagu
uucccucaggauagcuggcgcucucgcagacccgagccacgcaguuuuau
ccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccua
uucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgg
gcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcg
cugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucau
cagaccccagaaaagguguugguugauauagacagcaggaaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgccggcagucgagaguggacgggagccccgcggacgcuacgccgc
gacgaguaggagggccgcugcggugagccuugaagccuagggcgcgggcc
cggguggagccgccgcaggugcagaucuuggugguaguagcaaauauuca
aacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagcag
uugaacaugggucagucgguccugagagaugggcgagcgccguuccgaag
ggacgggcgauggccuccguugcccucggccgaucgaaagggagucgggu
ucagauccccgaauccggagcggagaugggcgccgcgaggcguccagugc
gguaacgcgaccgaucccggagaagccggcgggagccccggggagaguuc
ucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagag
aggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagc
ucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccgg
gccguacccauauccgcagcaggucuccaaggugaacagccucuggcaug
uuggaacaauguagguaagggaagucggcaagccggauccguaacuucgg
gauaaggauuggcucuaagggcugguagcagccgacuuagaacuggugcg
gaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccg
cggcggguguugacgcgaugugauuucugcccagugcucugaaugucaaa
gugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacuc
ucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaugaaug
gaugaacgagauucccacugucccuaccuacuauccagcgaaaccacagc
caagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagc
uugacucuagucuggcacggugaagagacguuuuuucacugacccgguga
ggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcgcccg
gccgcgcgccggccgggcgcgacccgcuccggggacagugccaggugggg
aguuugacuggggcgguacaccugucaaacgguaacgcagguguccuaag
gcgagcucagggaggacagaaaccucccguggagcagaagggcaaaagcu
cgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggccuc
acgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguua
ccacagggauaacuggcuuguggcggccaagcguucauagcgacgucgcu
uuuugauccuucgaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugauguguuguugccau
gguaauccugcucaguacgagaggaaccgcagguucagacauuuggugua
ugugcuuggcugaggagccaauggggcgaagcuaccaucugugggauuau
gacugaacgccucuaagucagaaucccgcccaggcggaacgauacggcag
cgccgcggagccucgguuggccucggauagccggucccccgcgggguccg
gugcggagugcccuucguccugggaaacggggcgcggccggagaggcggc
cgcccccucgcccgucacgcaccgcacguucguggggaaccuggcgcuaa
accauucguagacgaccugcuucugggucgggguuucguacguagcagag
cagcgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8glp mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): R12 L15 G17 R18 A21 K25 L28 R37 S44 Y48 R49 L52 L55 R59 K60 R61 M62 N63 N65 P66 S67 R68 P70 Y71 H72 F73 R74 R82 T83 R85 G86 M87 P89 H90 K91 K93 R94 Q96 F105 D106 G107 I108 P109 D113 K114 K115 K116 R117 M118 V126 V127 R128 L129 K130 P131 R133 K134 R140 E144 V145 G146 K148 Y149 L156 E157 K159 R160 K161 K163 A164 K165 H167 Y168 R169 K171 K172 M175 R176 K188 L201 V203
• Binding residue (residue number reindexed from 1): R11 L14 G16 R17 A20 K24 L27 R36 S43 Y47 R48 L51 L54 R58 K59 R60 M61 N62 N64 P65 S66 R67 P69 Y70 H71 F72 R73 R81 T82 R84 G85 M86 P88 H89 K90 K92 R93 Q95 F104 D105 G106 I107 P108 D112 K113 K114 K115 R116 M117 V125 V126 R127 L128 K129 P130 R132 K133 R139 E143 V144 G145 K147 Y148 L155 E156 K158 R159 K160 K162 A163 K164 H166 Y167 R168 K170 K171 M174 R175 K187 L200 V202

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0032496 response to lipopolysaccharide
• GO:0042592 homeostatic process
• GO:0048246 macrophage chemotaxis
• GO:0060425 lung morphogenesis
• GO:0071346 cellular response to type II interferon
• GO:1901194 negative regulation of formation of translation preinitiation complex

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0097452 GAIT complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8glp, PDBe:8glp, PDBj:8glp
• PDBsum: 8glp
• PubMed: 37020024
• UniProt: P40429|RL13A_HUMAN Large ribosomal subunit protein uL13 (Gene Name=RPL13A)