Structure of PDB 8ir1 Chain w Binding Site BS01

Receptor Information

>8ir1 Chain w (length=449) Species: 9606 (Homo sapiens)

STINPSKASTNPDRVMRDRATIRRLNMYRQKERRNSRGKIIKPLQYQSTV
ASGTVARVEPNIKWFGNTRVIKQSSLQKFQEEMDTVMKDPYKVVMKQSKL
PMSLLHDRIRPHNLKVHILDTESFETTFGPKSQRKRPNLFASDMQSLIEN
AEMSTESYDQGKDRDLVTEDTGVRNEAQEEIYKKGQSKRIWGELYKVIDS
SDVVVQVLDARDPMGTRSPHIETYLKKEKPWKHLIFVLNKCDLVPTWATK
RWVAVLSQDYPTLAFHASLTNPFGKGAFIQLLRQFGKLHTDKKQISVGFI
GYPNVGKSSVINTLRSKKVCNVAPIAGETKVWQYITLMRRIFLIDCPGVV
YPSEDSETDIVLKGVVQVEKIKSPEDHIGAVLERAKPEYISKTYKIDSWE
NAEDFLEKLAFRTGKLLKGGEPDLQTVGKMVLNDWQRGRIPFFVKPPNA

Ligand information

>8ir1 Chain 2 (length=3369)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacggcaaaucgguc
guccgaccuggguauaggggcgaaacuaaucaccaucuaguagcugguuc
ccuccgaaguuuccccaggauagcuggcgcucucgcgcaguuuuauccgg
uaaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgggcg
uggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcug
cgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucag
acccagaaaagguguugguugauauagacagcaggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuag
cccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgcc
ggcagucgagaguggacgggagcggcggcccggagccccgcggacgcuac
gccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgc
gggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaau
auucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaac
agcaguugaacaugggucagucgguccugagagaugggcgagcgccguuc
cgaacgaucgaaagggagucggguucagauccccgaauccggaguggcgg
agaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggaga
agccggcgggagccccggggagaguucucuuuucuuugugaagggcaggg
cgcccuggaauggguucgccccgagagaggggcccgugccuuggaaagcg
ucgcgguuccggcggcguccggugagcucucgcuggcccuugaaaauccg
ggggagaggguguaaaucucgcgccgggccguacccauauccgcagcagg
ucuccaaggugaacagccucuggcauguuggaacaauguagguaagggaa
gucggcaagccggauccguaacuucgggauaaggauuggcucuaagggcu
guagcagccgacuuagaacuggugcggaccaggggaauccgacuguuuaa
uuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcgaugugau
uucaaagugaagaaaucaaugaaggaguaacuaugacucucgguagccaa
augaacgagauucccacugucccuaccuacuauccagcgaaaccacagcc
aagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcu
ugacucuagucuggcacggugaaguuuuuucacugacccggugaggcggc
cgcuccggggacagugccagguggggaguuugagggcgguacaccuguca
aacgguaacgcagguguccuaaggcgagcucagggaggacagaaaccucc
cguggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaau
acagaccgugaaagcggggccucacgauccuucugaccuuuuggguuuua
agcaggaggugucagaaaaguuacagggauaggcuuguggcggccaagcg
uucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucau
ugugaagcagaauucaccaagcguuggauuguucacccacuaauagggaa
cgugagcuggguuagaccgucgugagacagguuaguuuuacccuacugau
gauguguuguugccaugguaauccugcucaguacgagaggaaccgcaggu
ucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcua
ccaucugugggauuaugacugaacgccucuaagucagaaucccgcccagg
cggaacgauacggcagcgccgcggagccucgguuggccucggauagccgg
ucccccgccgggguccggugcggagugcccuucguccugggaaacggggc
gcggccggagaggcggccgcccccucgcccgucacgcaccgcacguucgu
ggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggg
uuucguacguagcagagcagcucccucgcugcgaucuauugaaagucagc
ccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ir1 Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): S10 T11 K16 A17 S18 T19 R23 M32 R33 R39 R45 R49 N51 S52 R53 I57 K58 S68 G69 N77 I78 K79 R85 K112 N129 L130 Q149 K151 R180 E196 K200 S203 K204 R205 I206 W207 Y211 W247 D258 L259 V260 P261 T262 W263 A264 R267 W268 V271 L285 K309 Q310 R331 K334 V335 A342 Q349 Y350 T352 Y367 Q383 E385 K386 Y405 T429 K431 L432 L433 K434 G435 Q441 M446 R453 G454 R455 I456 F458 F459 V460 K461 P462 P463 A465
• Binding residue (residue number reindexed from 1): S1 T2 K7 A8 S9 T10 R14 M16 R17 R23 R29 R33 N35 S36 R37 I41 K42 S52 G53 N61 I62 K63 R69 K96 N113 L114 Q133 K135 R164 E180 K184 S187 K188 R189 I190 W191 Y195 W231 D242 L243 V244 P245 T246 W247 A248 R251 W252 V255 L269 K293 Q294 R315 K318 V319 A326 Q333 Y334 T336 Y351 Q367 E369 K370 Y389 T413 K415 L416 L417 K418 G419 Q425 M430 R437 G438 R439 I440 F442 F443 V444 K445 P446 P447 A449

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:8ir1, PDBe:8ir1, PDBj:8ir1
• PDBsum: 8ir1
• PubMed: 37491604
• UniProt: Q13823|NOG2_HUMAN Nucleolar GTP-binding protein 2 (Gene Name=GNL2)