Structure of PDB 8idy Chain 4 Binding Site BS02

Receptor Information

>8idy Chain 4 (length=611) Species: 9606 (Homo sapiens)

AHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHRIRHFYMRKV
KFTQQNYHDRLSQILTDFPKLDDIHPFYADLMNILYDKDHYKLALGQINI
AKNLVDNVAKDYVRLMKYGDSLYRCKQLKRAALGRMCTVIKRQKQSLEYL
EQVRQHLSRLPTIDPNTRTLLLCGYPNVGKSSFINKVTRADVDVQPYAFT
TKSLFVGHMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAV
LYVMDLSEQCGHGLREQLELFQNIRPLFINKPLIVVANKCDVKRIAELSE
DDQKIFTDLQSEGFPVIETSTLTEEGVIKVKTEACDRLLAHRVETKMKGN
KVNEVLNRLHLAIPTRRDDKERPPFIPEGVVARRKRMETEESRKKRERDL
ELEMGDDYILDLQKYWDLMNLSEKHDKIPEIWEGHNIADYIDPAIMKKLE
ELEKEEELRTAAGEYDSVSESEDEEMLEIRQLAKQIREKKKLKILESKEK
NTQGPRMPRTAKKVQRTVLEKEMRSLGVDMDDKDDAHYAVQARRSRSSRT
PRDVSGLRDVKMVKKAKTMMKNAQKKMNRLGKKGEADRHVFDMKPKHLLS
GKRKAGKKDRR

Ligand information

>8idy Chain 2 (length=3641)

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
cgacgcccgccacgcaguuuuauccgguaaagcuuuaaauggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguu
aaggcgcccgaugccgacgcucaucagaccccagaaaagguguugguuga
uauagacagcaggacgguggccauggaagucggaauccgcuaaggagugu
guaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugg
agcgucgggcccauacccggccgucgccggcagucgagaguggacgggag
cggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggccg
cugcggugagccuugaagccuagggcgcgggcccggguggagccgccgca
ggugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaagg
ccgaaguggagaaggguuccaugugaacagcaguugaacaugggucaguc
gguccugagagaugggcgagcgccguuccgaagggacgggcgauggccuc
cguugcccucggccgaucgaaagggagucggguucagauccccgaauccg
gaguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccga
ucccggagaagccggcgggagccccggggagaguucucuuuucuuuguga
agggcagggcgcccuggaauggguucgccccgagagaggggcccgugccu
uggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuu
gaaaauccgggggagaggguguaaaucucgcgccgggccguacccauauc
cgcagcaggucuccaaggugaacagccucuggcauguuggaacaauguag
guaagggaagucggcaagccggauccguaacuucgggauaaggauuggcu
cuaagggcugggucggucgcggccggcgccuagcagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgugaacgagauu
cccacugucccuaccuacuauccagcgaaaccacagccaagggaacgggc
uuggcggaaucagcggggaaagaagacccuguugagcuugacucuagucu
ggcacggugaagagacaugagagguguagaauaagugggaggcccccggc
gcccccccgguguccccgcgaggggcccggggcgggguccgccggcccug
cgggccgccggugaaauaccacuacucugaucguuuuuucacugacccgg
ugaggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcgc
ccggccgcgcgccggccgggcgcgacccgcuccggggacagugccaggug
gggaguuugacuggggcgguacaccugucaaacgguaacgcagguguccu
aaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaaa
gcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggc
cucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaag
uuaccacagggauacuuguggcggccaagcguucauagcgacgucgcuuu
gaugucggcucuuccuaucauugugaagcagaauucaccaagcguuggau
uguucacccacuaauagggaacgugagcuggguuuagaccgucgugagac
agguuaguuuuacccuacugaugauguguuguugccaugguaauccugcu
caguacgagaggaaccgcagguucagacauuugguguaugugcuuggcug
aggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccu
cuaagucagaaucccgcccaggcggaacgauacggcagcgccgcggagcc
ucgguuggccucggauagccggucccccgccgggguccggugcggagugc
ccuucguccugggaaacggggcgcggccggagaggcggccgcccccucgc
ccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucguag
acgaccugcuucugggucgggguuucguacguagcagagcagcucccucg
cugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8idy Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): Y4 K7 V11 D20 L23 K25 Q27 R28 K29 T32 V33 I34 K36 H41 R42 R49 K50 Q98 I101 L105 K118 R125 K127 K130 R131 G135 R136 C138 T139 R143 Q144 R155 Q156 R160 R190 Q196 Y198 F200 V207 H209 R216 R399 K491 K494 I495 S498 K499 K501 Q504 R510 R545 P574 R575 K588 M592 K594 N595 Q597 K599 N601 G604 K605 K606 R611 D615 H620 K625 R626 K627 A628 G629 K631 D632 R633 R634
• Binding residue (residue number reindexed from 1): Y3 K6 V10 D19 L22 K24 Q26 R27 K28 T31 V32 I33 K35 H40 R41 R48 K49 Q97 I100 L104 K117 R124 K126 K129 R130 G134 R135 C137 T138 R142 Q143 R154 Q155 R159 R189 Q195 Y197 F199 V206 H208 R215 R398 K490 K493 I494 S497 K498 K500 Q503 R509 R544 P551 R552 K565 M569 K571 N572 Q574 K576 N578 G581 K582 K583 R588 D592 H597 K602 R603 K604 A605 G606 K608 D609 R610 R611

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:1990275 preribosome binding

Biological Process

• GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity
• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0001649 osteoblast differentiation
• GO:0008156 negative regulation of DNA replication
• GO:0008285 negative regulation of cell population proliferation
• GO:0022408 negative regulation of cell-cell adhesion
• GO:0030336 negative regulation of cell migration
• GO:0031397 negative regulation of protein ubiquitination
• GO:0033342 negative regulation of collagen binding
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis
• GO:0050821 protein stabilization

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0031965 nuclear membrane
• GO:0048471 perinuclear region of cytoplasm

External links

• PDB: RCSB:8idy, PDBe:8idy, PDBj:8idy
• PDBsum: 8idy
• PubMed: 37491604
• UniProt: Q9BZE4|GTPB4_HUMAN GTP-binding protein 4 (Gene Name=GTPBP4)