Structure of PDB 8ipx Chain w Binding Site BS01

Receptor Information

>8ipx Chain w (length=433) Species: 9606 (Homo sapiens)

SKASTNPDRVQGAGGQNMRDRATIRRLNMYRQKERRNSRGKIIKPLQYQS
TVASGTVARVEPNIKWFGNTRVIKQSSLQKFQEEMDTVMSKLPMSLNLKV
HILDTESFETTFGPKSQRKRPNLFASDMQSLIENAEMSTESYDQGKDRDL
VTEDTGVRNEAQEEIYKKGQSKRIWGELYKVIDSSDVVVQVLDARDPMGT
RSPHIETYLKKEKPWKHLIFVLNKCDLVPTWATKRWVAVLSQDYPTLAFH
ASLTNPFGKGAFIQLLRQFGKLHTDKKQISVGFIGYPNVGKSSVINTLRS
KKVCNVAPIAGETKVWQYITLMRRIFLIDCPGVVYPSEDSETDIVLKGVV
QVEKIKSPEDHIGAVLERAKPEYISKTYKIDSWENAEDFLEKLAFRTGKL
LKGGEPDLQTVGKMVLNDWQRGRIPFFVKPPNA

Ligand information

>8ipx Chain 2 (length=3475)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacgugcaaaucggu
cguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcu
gguucccuccgaaguuucccucaggauagcuggcgcucucgcagacccga
cgcccgccacgcaguuuuauccgguauggguaagaagcccggcucgcugg
cguggagccgggcguggaaugcgagugccuagugggccacuuuugguaag
cagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaug
ccgacgcucaucagacccagaaaagguguugguugauauagacagcagga
cgguggccauggaagucggaauccgcuaaggaguguguaacaacucaccu
gccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccau
acccggccgucgccggcagucgagaguggacgggagcggcggcccggagc
cccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagccuu
gaagccuagggcgcgggcccggguggagccgccgcaggugcagaucuugg
ugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggagaag
gguuccaugugaacagcaguugaacaugggucagucgguccugagagaug
ggcgagcgccguuccgaagggacgggcgauggccugcccuccgaucgaaa
gggagucggguucagauccccgaauccggaguggcggagaugggcgccgc
gaggcguccagugcgguaacgcgaccgaucccggagaagccggcgggagc
cccggggagaguucucuuuucuuugugaagggcagggcgcccuggaaugg
guucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggc
ggcguccggugagcucucgcuggcccuugaaaauccgggggagagggugu
aaaucucgcgccgggccguacccauauccgcagcaggucuccaaggugaa
cagccucuggcauguuggaacaauguagguaagggaagucggcaagccgg
auccguaacuucgggauaaggauuggcucuaagggcugggucggucgcgg
ccggcgccuagcagccgacuuagaacuggugcggaccaggggaauccgac
uguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcg
augugauuucugcccagugcucugaaugucaaagugaagaaauucaauga
agcgcggguaaacggcgguuaagaacgagauucccacugucccuaccuac
uauccagcgaaaccacagccaagggaacgggcuuggcggaaucagcgggg
aaagaagacccuguugagcuugacucuagucuggcacggugaaguuuuuu
cacugacccggugaggcgggggggcgagccccgaggggcucucgcuucug
gcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggac
agugccagguggggaguuuccugucgcagguguccuaaggcgagcucagg
gaggacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuu
gauuuuuacgaauacagaccgugaaagcggggccgauccuucugaccuuu
uggguuuuaagcaggagguaaguuaccacagggauaggcuuguggcggcc
aagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acugaugauguguuguugccaugguaauccugcucaguacgagaggaacc
gcagguucagacauuugguguaugugcuuggcugaggagccaauggggcg
aagcuaccaucugugggauuaugacugaacgccucuaagucagaaucccg
cccaggcggaacgauacggcagcgccgcggagccucgguuggccucggau
agccggucccccgccgggguccggugcggagugcccuucguccugggaaa
cggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcac
guucguggggaaccuggcgcuaaaccauucguagacgaccugcuucuggg
ucgggguuucguacguagcagagcagcucccucgcugcgaucuauugaaa
gucagcccucgacacaaggguuugu

.........................<<<<<<.....<......>......
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..>>>>>..<<<<<<<<<<...<<<<<<<<........<<<<<<<<....
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>>...>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....(((((..<<<<<<)))))..]]]..................
................<<....>>...............<<<......>>
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<...<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<.......<<
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>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<
.<<<<...<<..<<<..<.<<<<......<<<<<<<<..>>>>>>>>...
....>>>>.>.>>>........>>>>>>...>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<.<<.<<<<<<<<<<.<<<<<<.<<<<<................>>>>
>.>>>>>.>.>>>>>>>.>>>...>>.>..>>>>.>>..<<<<<<<<<..
.....>>>>>>>.>>....>>>>>>.....>>>.>>>>>...>>>>>...
>>>>>>>>..<<<<.....>>>><<<<<<....<<<<<<<<<<<<<..<<
<...<<<<........>>>>.....>>>...<<....>>...<<<<<<<.
.....>>>>>>>..<<<<<...<<<..<<<..[[....(((>>>..>>>.
...>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>
>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<
<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>>.
>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..>.
>>..<<<<<<....<.<........>.><<<<<<<<<<............
..........<<<.<<<<<<.........>>>>...<<<<<<<<<.....
....>>>>>>>>>....>>>>>>>>>>>>.>>>..<<<<.<<<<<.....
>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((.....
..<<<<<.....<<.........<<<.<<<<<<<<<<.......<<<<<.
<<....<<.........>>....>>.........<<......>>...>>>
>>...>>>>>>>>>>>>>..........))).>>...>>>>>..>>>...
>>>>>>><<<<<<.<<<..........)))....]]..............
..............>>>>>>>>>....>>>>>>.<<<<<<<<<<.<<...
...<<<<.<<<<....>>>>>>>>...>>>>>>>>>>.>>.....>>>>>
><<<....<<.....<<<<<<.......>>>>>>.<<<.....<<<<<.<
<...<<<<<....<<.....>>..>>>>>....((<<<<<<...<<....
<<<....>>>.............<<<<........>>>>.....>>....
>>>..<<<<<........>>>>>))<<<<....<<<<<...<<<<<<<..
..>>>>>>>...<<<....>>>...<..<<<<<<<...<<<<<<<<<<<<
<<<<<<<<<<<..{{{..>>>>>>....<<<<<.<<<<.<<<<.....<<
<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<.......>>
>>>>>>>>>.>.>>>>>>>>>>>>.........>>>>>>>..>.......
...>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<...
..>>>>..>>>....<<<<.....<<<<<<<.<<...............<
<<<<....<<..>>.....>>>>><<.<<<<<<<<<<<..<.........
...>.......>>>>>..>>>>>>.>>............<<<<<<<<<..
<<<.........>>>..<<<<<<<....<<<<.....>>>>......>>>
>>>>.......<<<..<<<<<<....<<<.....<<<<....>>>>....
.>>>.>>>>..>>>>>.........>>.>>>>>>>.....>>.>>>>>>>
..>>>>>>...>>>....<<<<<........>>>>>....(((((..{{{
........(((((.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<...>>>
>>>...<<<<<.....<<<<.....<..............>.........
.......<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>...
.>>>>>>>>>..>>>>>...<<......>>.........<<<<<<...<<
<<<<.......>>>>>>...........((......>>>>>>....<<<.
.<<<<....>>>>..>>>.<<<....>>>...))....(((((...(((.
.>>>>>>.))).)))))...]]]]..}})))))..........<<<<<<.
................>>>>>>.................<<<<.<<<<<<
..<.<.<<<<<......>>>>>...>.>.<<<.........>>>.....>
>>>>..>...>>>>......<<<<<<<....>>>.>>>>........}}}
.))))).....<<<<<<.<..<<<..<.<<<<<.................
>>>>>.><<<<....<<<<....<<.<<<<<<.}}}..>>>>..>>.>>.
..>>>>...>>>><<<<<...<<<<<...........>>>>>...>>>>>
.>>>...>.>>>>>>.....<<<<<<<.<<..<<<<....<<<.......
.<<<<<.<<<<....>>>>.>>>>>.......>>>...<<<..<<<<...
.<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>........
......>>>>..>>>>>>>>><<<<<.<.............>....<<.<
<<<<<<.<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>
>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ipx Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 4.3 Å
• Binding residue (original residue number in PDB): S18 T19 Q30 N31 M32 R33 R45 R50 N51 R53 I57 S68 G69 L130 K131 H133 I134 K147 K151 R152 E196 K200 S203 K204 R205 I206 W207 Y211 K291 I295 Q296 R299 V335 P340 I341 G343 W348 Q349 Y350 T352 M354 R355 Q383 E385 K386 T429 K431 L432 L433 G435 Q441 T442 K445 M446 R453
• Binding residue (residue number reindexed from 1): S4 T5 Q16 N17 M18 R19 R31 R36 N37 R39 I43 S54 G55 L98 K99 H101 I102 K115 K119 R120 E164 K168 S171 K172 R173 I174 W175 Y179 K259 I263 Q264 R267 V303 P308 I309 G311 W316 Q317 Y318 T320 M322 R323 Q351 E353 K354 T397 K399 L400 L401 G403 Q409 T410 K413 M414 R421

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003924 GTPase activity
• GO:0005525 GTP binding

Biological Process

• GO:0008150 biological_process
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0016020 membrane

External links

• PDB: RCSB:8ipx, PDBe:8ipx, PDBj:8ipx
• PDBsum: 8ipx
• PubMed: 37491604
• UniProt: Q13823|NOG2_HUMAN Nucleolar GTP-binding protein 2 (Gene Name=GNL2)