Structure of PDB 8g61 Chain LB Binding Site BS01

Receptor Information

>8g61 Chain LB (length=402) Species: 9606 (Homo sapiens)

SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKA
GMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRT
FKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFS
SMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERL
EQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKV
ACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSL
LVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEE
GA

Ligand information

>8g61 Chain L5 (length=3657)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccgcgggggaccgucccccgaccggcgaccggccgccg
ccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggc
ugggaaggcccggcggggaagguggcucgggggccccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccugggggggccgggccaccccucccacggcgcg
accgcucggggcggacuguccccagugcgccccgggcgggucgcgccguc
gggcccggggggccacgcgcgcgucccccgaagagggggacggcggagcg
agcgcacggggucggcggcgacgucggcuacccacccgacccgucuugaa
acacggaccaaggagucuaacacgugcgcgagucgggggcucgcacgaaa
gccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgaggu
gggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgucu
cgcccgccgcgccggggagguggagcacgagcgcacguguuaggacccga
aagauggugaacuaugccugggcagggcgaagccagaggaaacucuggug
gagguccguagcgguccugacgugcaaaucggucguccgaccuggguaua
ggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaaguuu
cccucaggauagcuggcgcucucgcagacccgaacgcaguuuuauccggu
aaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauucuc
aaacuuuaaauggguaagaagcccggcucgcuggcguggagccgggcgug
gaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugcg
ggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagac
cccagaaaagguguugguugauauagacagcaggacgguggccauggaag
ucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcagucgagaguggacgggagcggccccgcggacgcuacgccgcgacgag
uaggagggccgcugcggugagccuugaagccuagggcgcgggcccgggug
gagccgccgcaggugcagaucuuggugguaguagcaaauauucaaacgag
aacuuugaaggccgaaguggagaaggguuccaugugaacagcaguugaac
augggucagucgguccugagagaugggcgagcgccguuccgaagggacgg
gcgauggccuccguugcccucggccgaucgaaagggagucggguucagau
ccccgaauccggagcggagaugggcgccgcgaggcguccagugcgguaac
gcgaccgaucccggagaagccggcgggagccccggggagaguucucuuuu
cuuugugaagggcagggcgcccuggaauggguucgccccgagagaggggc
ccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucucgc
uggcccuugaaaauccgggggagaggguguaaaucucgcgccgggccgua
cccauauccgcagcaggucuccaaggugaacagccucuggcauguuggaa
caauguagguaagggaagucggcaagccggauccguaacuucgggauaag
gauuggcucuaagggcugguagcagccgacuuagaacuggugcggaccag
gggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgg
guguugacgcgaugugauuucugcccagugcucugaaugucaaagugaag
aaauucaaugaagcgcggguaaacggcgggaguaacuaugacucucuuaa
gguagccaaaugccucgucaucuaauuagugacgcgcaugaauggaugaa
cgagauucccacugucccuaccuacuauccagcgaaaccacagccaaggg
aacgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacu
cuagucuggcacggugaagagacaugagagguguagaauaagugggaggc
ccgggccgccggugaaauaccacuacucugaucguuuuuucacugacccg
gugaggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcg
cccggccgcgcgccggccgggcgcgacccgcuccggggacagugccaggu
ggggaguuugacuggggcgguacaccugucaaacgguaacgcaggugucc
uaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaa
agcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcgggg
ccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaa
guuaccacagggauaacuggcuuguggcggccaagcguucauagcgacgu
cgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaau
ucaccaagcguuggauuguucacccacuaauagggaacgugagcuggguu
uagaccgucgugagacagguuaguuuuacccuacugaugauguguuguug
ccaugguaauccugcucaguacgagaggaaccgcagguucagacauuugg
uguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggga
uuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauacg
gcagcgccgcggagccucgguuggccucggauagccggucccccgccggg
guccggugcggagugcccuucguccugggaaacggggcgcggccggagag
gcggccgcccccucgcccgucacgcaccgcacguucguggggaaccuggc
gcuaaaccauucguagacgaccugcuucugggucgggguuucguacguag
cagagcagcucccucgcugcgaucuauugaaagucagcccucgacacaag
gguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g61 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.94 Å
• Binding residue (original residue number in PDB): S2 H3 K5 F6 S7 A8 P9 R10 H11 G12 S13 L14 G15 F16 L17 P18 R19 K20 R21 S23 H25 R26 K28 K30 S31 K50 M53 T54 H55 R62 P63 G64 S65 A75 Y92 T95 R97 L99 R100 T101 F102 K103 T104 R116 R117 F118 Y119 K120 H123 K126 K128 F130 K132 Y133 Y156 R174 Q175 K176 K177 E182 T223 K224 G225 K226 G227 Y228 K229 G230 R234 K238 K239 R242 K243 T244 H245 R246 G247 L248 R249 K250 V251 A252 C253 I254 G255 A256 W257 H258 P259 A260 R261 V262 S265 R268 A269 Q271 Y274 H276 R277 T278 E279 I280 N281 L317 G318 H322 G324 E325 K334 G335 C336 V337 V338 T340 K341 K342 R343 L351 L352 R357 S372 K373 F374 G375 H376 K385 M389 L392 K393
• Binding residue (residue number reindexed from 1): S1 H2 K4 F5 S6 A7 P8 R9 H10 G11 S12 L13 G14 F15 L16 P17 R18 K19 R20 S22 H24 R25 K27 K29 S30 K49 M52 T53 H54 R61 P62 G63 S64 A74 Y91 T94 R96 L98 R99 T100 F101 K102 T103 R115 R116 F117 Y118 K119 H122 K125 K127 F129 K131 Y132 Y155 R173 Q174 K175 K176 E181 T222 K223 G224 K225 G226 Y227 K228 G229 R233 K237 K238 R241 K242 T243 H244 R245 G246 L247 R248 K249 V250 A251 C252 I253 G254 A255 W256 H257 P258 A259 R260 V261 S264 R267 A268 Q270 Y273 H275 R276 T277 E278 I279 N280 L316 G317 H321 G323 E324 K333 G334 C335 V336 V337 T339 K340 K341 R342 L350 L351 R356 S371 K372 F373 G374 H375 K384 M388 L391 K392

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0071353 cellular response to interleukin-4

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• 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:8g61, PDBe:8g61, PDBj:8g61
• PDBsum: 8g61
• PubMed: 37020024
• UniProt: P39023|RL3_HUMAN Large ribosomal subunit protein uL3 (Gene Name=RPL3)