Structure of PDB 6lqm Chain D Binding Site BS01

Receptor Information

>6lqm Chain D (length=358) Species: 9606 (Homo sapiens)

CARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPY
AVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMF
APTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELPL
VVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRI
QRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIW
TESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQRAL
RAPRKKIHRRVLKKNPLKNLRIMLKLNPYATMRRNTILRQARNHKLRVDK
AAAAAAAL

Ligand information

>6lqm Chain 2 (length=3532)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggccua
uucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgg
gcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcg
cugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucau
cagaccccagaaaagguguugguugauauagacagcccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcagucgagaguggacgggagcggcggcccggagccccgcggacgcuacg
ccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcg
ggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaaua
uucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaaca
gcaguugaacaugggucagucgguccugagagaugggcgagcgccguucc
gaagggacgggcgauggccuccguugcccucggccgaucgaaagggaguc
ggguucagauccccgaauccggaguggcggagaugggcgccgcgaggcgu
ccagugcgguaacgcgaccgaucccggagaagccggcgggagccccgggg
agaguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcc
ccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggcgucc
ggugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucuc
gcgccgggccguacccauauccgcagcaggucuccaaggugaacagccuc
uggcauguuggaacaauguagguaagggaagucggcaagccggauccgua
acuucgggauaaggauuggcucuaagggcuggagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgguuaagguagcca
aaugccucgucaucuaauuagugacgcgcaugaauggaugaacgagauuc
ccacugucccuaccuacuauccagcgaaaccacagccaagggaacgggcu
uggcggaaucagcggggaaagaagacccuguugagcuugacucuagucug
gcacggugaaguuuucacugacccggugaggcgggggggcgagccccgag
gggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcg
acccgcuccggggacagugccagguggggaguuugacuggggcgguacac
cugucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaa
accucccguggagcagaagggcaaaagcucgcuugaucuugauuuucagu
acgaauacagaccgugaaagcggggccucacgauccuucugaccuuuugg
guuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugu
ggcggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggc
ucuuccuaucauugugaagcagaauucaccaagcguuggauuguucaccc
acuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguu
uuacccuacugaugauguguuguugccaugguaauccugcucaguacgag
aggaaccgcagguucagacauuugguguaugugcuuggcugaggagccaa
uggggcgaagcuaccaucugugggauuaugacugaacgccucuaagucag
aaucccgcccaggcggaacgauacggcagcgccgcggagccucgguuggc
cucggauagccggucccccgccgggguccggugcggagugcccuucgucc
ugggaaacggggcgcggccggagaggcggccgcccccucgcccgucacgc
accgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugc
uucugggucgggguuucguacguagcagagcagcucccucgcugcgaucu
auugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lqm Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.
• Resolution: 3.09 Å
• Binding residue (original residue number in PDB): A4 R33 F39 T42 N43 R45 K46 N47 N48 R49 Q50 Y52 V54 S55 A58 H60 Q61 T62 S63 T69 G70 R71 A72 V73 A74 R75 P77 R80 G82 G83 T84 R86 Q89 N94 M95 R97 R100 M101 F102 A103 K106 W108 R109 R110 R114 N116 T118 Q119 K120 R121 K140 K163 T164 K165 K172 N178 K182 Y184 R188 M189 R190 A191 K193 K195 M196 R197 R199 R204 R205 K219 R222 N223 K239 P242 G243 H245 K274 S275 R291 L293 K294 P305 R306 K307 K308 H310 R311 R312 L314 K316 N321 L322 R323 L326 K327 M335 R336 T339 R342 Q343 N346 R350 K353
• Binding residue (residue number reindexed from 1): A2 R31 F37 T40 N41 R43 K44 N45 N46 R47 Q48 Y50 V52 S53 A56 H58 Q59 T60 S61 T67 G68 R69 A70 V71 A72 R73 P75 R78 G80 G81 T82 R84 Q87 N92 M93 R95 R98 M99 F100 A101 K104 W106 R107 R108 R112 N114 T116 Q117 K118 R119 K138 K161 T162 K163 K170 N176 K180 Y182 R186 M187 R188 A189 K191 K193 M194 R195 R197 R202 R203 K217 R220 N221 K237 P240 G241 H243 K272 S273 R289 L291 K292 P303 R304 K305 K306 H308 R309 R310 L312 K314 N319 L320 R321 L324 K325 M332 R333 T336 R339 Q340 N343 R347 K350

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

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005791 rough 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:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lqm, PDBe:6lqm, PDBj:6lqm
• PDBsum: 6lqm
• PubMed: 32669547
• UniProt: P36578|RL4_HUMAN Large ribosomal subunit protein uL4 (Gene Name=RPL4)