Structure of PDB 8fks Chain SR Binding Site BS01

Receptor Information

>8fks Chain SR (length=428) Species: 9606 (Homo sapiens)

AHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHRIRHFYMRKV
KFTQQNYHDRLSQILTDFPKLDDIHPFYADLMNILYDKDHYKLALGQINI
AKNLVDNVAKDYVRLMKYGDSLYRCKQLKRAALGRMCTVIKRQKQSLEYL
EQVRQHLSRLPTIDPNTRTLLLCGYPNVGKSSFINKVTRADVDVQPYAFT
TKSLFVGHMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAV
LYVMDLSEQCGHGLREQLELFQNIRPLFINKPLIVVANKCDVKRIAELSE
DDQKIFTDLQSEGFPVIETSTLTEEGVIKVKTEACDRLLAHRVENRLHLA
IPTRRDDKERPPFIPEGVDYILDLQKYWDLMNLSEKHDKIPEIWEGHNIA
DYIDPAIMKKLEELEKEEELRTAAGEYD

Ligand information

>8fks Chain L3 (length=1824)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagaggacgggugggguccgcgcaguccgcccggaggau
ucaacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcgc
cgcgaccggcuccgggacggcugggaaggcccggcggggaagguggcucg
ggcccgaguguuacagcccccccggcagcagcacucgccgaaucccgggg
ccgagggagcgccgcgcucuccggccgggccaggccacgcgagcgcacgg
ggucggcggcgacgucggcuacccacccgacccgucuacacggaccaagg
agucuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgc
aaggugggaucccgaggcgccgagggcgcaccaccggcccgucucgcccg
gggagguggagcacgagcgcacguguuaggacccgaaagauggugaacca
ucuaguagcugguucccuccgaaguuucccucaggauagcuggcgcucuc
cgcaguuuuauccgggguaagaagcccggcucgagccgggcguggaaugc
gagugccuagugggccacuuuugguaagcagaacuggcgcugcgggauga
accgaacgccggguuaaggcgcccgaugccgacgcucacccagaaaaggu
guugguugauauagacagcaggacgguggccauggaagucggaauccgcu
aaggaguguguaacaacucaccugccgaaucaacuagcccugaaaaugga
uggcgcuggagcgucgggcccauacccggccgucgccggcagucacgcua
cgccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcg
cgggcccggguggagccgccgcaggugcagaucuuggugguaguagcaau
guuggaacaauguaggaccuacuauccagcgaaaccagccaagcuuggcu
cagcggggcuggcuuguggcggccaagcgcgacgucgcuuuuugauugug
aagcagaauucaccaacccuacugaugguuguugccaugguaauccugcu
caguacgagaggaaccgcagguucagacauuugguguaugugcuuggcug
aggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccu
cuaagucagaaucccgcccaggcggaacgauagcgccgcggagccucggu
uggccucggauagccgguccccgggguccggugcggagugcccuucgucc
ugggaaacggggcgcggccggagaggcggccgcccccucgcccgucacgc
accgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugc
ugggucgggguuucguacguagcagagcagcucccucgcugcgaucuauu
gaaagagcccucgacacgguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fks Principles of human pre-60 S biogenesis.
• Resolution: 2.88 Å
• Binding residue (original residue number in PDB): K7 L21 L23 S24 Q27 K36 K50 L66 P70 K71 Y92 K93 L94 L96 Q98 I101 L105 K127 Q128 K130 R131 A132 L134 G135 R136 V140 Q144 R155 T163 R190 Y198 F200 V207 G208 H209
• Binding residue (residue number reindexed from 1): K6 L20 L22 S23 Q26 K35 K49 L65 P69 K70 Y91 K92 L93 L95 Q97 I100 L104 K126 Q127 K129 R130 A131 L133 G134 R135 V139 Q143 R154 T162 R189 Y197 F199 V206 G207 H208

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:8fks, PDBe:8fks, PDBj:8fks
• PDBsum: 8fks
• PubMed: 37410842
• UniProt: Q9BZE4|GTPB4_HUMAN GTP-binding protein 4 (Gene Name=GTPBP4)