Structure of PDB 8fkw Chain SR Binding Site BS01

Receptor Information

>8fkw Chain SR (length=462) Species: 9606 (Homo sapiens)

AHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHRIRHFYMRKV
KFTQQNYHDRLSQILTDFPKLDDIHPFYADLMNILYDKDHYKLALGQINI
AKNLVDNVAKDYVRLMKYGDSLYRCKQLKRAALGRMCTVIKRQKQSLEYL
EQVRQHLSRLPTIDPNTRTLLLCGYPNVGKSSFINKVTRADVDVQPYAFT
TKSLFVGHMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAV
LYVMDLSEQCGHGLREQLELFQNIRPLFINKPLIVVANKCDVKRIAELSE
DDQKIFTDLQSEGFPVIETSTLTEEGVIKVKTEACDRLLAHRVETKMKGN
KVNEVLNRLHLAIPTRRDDKERPPFIPEGVVARRKRMETEESRKKRERDL
ELEMGDDYILDLQKYWDLMNLSEKHDKIPEIWEGHNIADYIDPAIMKKLE
ELEKEEELRTAA

Ligand information

>8fkw Chain L3 (length=2277)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagaggaacgggugggguccgcgcaguccgcccggagga
uucaacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcg
ccgcgaccggcuccgggacggcugggaaggcccggcggggaagguggcuc
gggcccgaguguuacagcccccccggcagcagcacucgccgaaucccggg
gccgagggagcgccgcgcucuccggccgggccaggccacggagcgcacgg
ggucggcggcgacgucggcuacccacccgacccgucuugaaacacggacc
aaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccgug
gcgcaaggugggaucccgaggcccgccgagggcgcaccaccggcccgucu
cgcccggggagguggagcacgagcgcacguguuaggacccgaaagauggu
gaaaccaucuaguagcugguucccuccgaaguuucccggauagcuggcgc
ucuccgcaguuuuauccgguggguaagaagcccggcucgagccgggcgug
gaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugcg
ggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagac
cccagaaaagguguugguugauauagacagcaggacgguggccauggaag
ucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcagucacgcuacgccgcgacgaguaggagggccgcugcggugagccuug
aagccuagggcgcgggcccggguggagccgccgcaggugcagaucuuggu
gguaguagcauucaaacgagaacuuugaaggccgaaguggagaaggggcg
auggccuccggcccucgcggagaugggcgccgcgaggcguccagugaauc
ucgcccgcagcaggucuccggugaacagccucuggcaauguagguaaggg
aagucgggaauccgauucccacugucccuaccuacuauccagcgaaacca
cagccaagggaacgggcuuggcggaaucagcggggagaagacccuguuga
gcuugacucuagucuggcacggugaagagacaugagagguguagaauaag
ugggaggcggccgccggugaaauaccacuacucugaucguuuuuuccagu
gccagguggggaguuauccuucugaccuuuuggguuuuaagcaggaggug
ucagaaaaguuaccacagggauaacuggcuuguggcggccaagcgcgacg
ucgcuuuuugaugaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggggaccgu
cgugagacagguucccuacugaugguuguugccaugguaauccugcucag
uacgagaggaaccgcagguucagacauuugguggugcuuggcugaggagc
caauggggcgaagcuaccaucugugggauuaugacugaacgccucuaagu
cagaaucccgcccaggcggaacgauaagcgccgcggagccucgguuggcc
ucggauagccgguccccgggguccggugcggagugcccuucguccuggga
aacggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgc
acguucguggggaaccuggcgcuaaaccauucguagacgaccugcuucug
ggucgggguuucguacguagcagagcagcucccucgcugcgaucuauuga
aagucagcccucgacacaaggguuugu

........................<<<<<<...............>>>>>
.>.........<<....>>..<<<<<<.....<<.....>>....>>>>>
>..<<<..<<<<<...<<<<<<<<<<.>>>>>>.>>>>.....>>>>>..
<<<<<<<<<<...<<<<<<<<.<<.....<<<<<<<<....<<<<.....
.>>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>
>>>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....
<<<<<<.>>>>>>..>>>................................
..<<....>>...............<<<<....>>>>.............
...................<<<<<<<<.<<<<.<<...<<<<<<<<.<<<
.....<<<<<<<<<<..>>>>>>>>>>......>>>.>>>.>>>>>...<
<<<<<<.<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<......<<<<
<<..>>>>>>.......>>>>>>.>>>........>>>>>>..>>>>>>>
>>>>..........<<<<<<.<..>.<<<<<<.>>>>.>>>>>>>>....
..>>.>>>>>...>>>>>..>>>>>>>>>..<<<<.<....>.>>>><<<
<<<....<<<<<<<<<<<<<..<<<...<<<<........>>>>.....>
>>....<<<<<...<<<..<<<..>>>..>>>....>>>>>.<<<<<<<<
<.<<..>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<...<<<<<<
...>>>>>>......>.>>..<<<<<<......<<<.>>>..<<.<<<<<
<<...<<<.<<<<<<<<...>>>>>>...<<<<<<<<..>>>>>>>>...
.>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>>>>....<<
<......>>>...<<<<<<<...<<<(((.......<<<<<.....<<..
........<<<.<<<<<<<<<<.....<.<<<<<.<<<...<<.......
..>>...>>>.........<<......>>...>>>>>.>.>>>>>>>>>>
>>>..........))).>>...>>>>>..>>>...>>>>>>><<<<<<.<
<<...........>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<....
..<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..>.....>>>>>>
<<.....<<.<<<<<<.......>>>>>>.<<<<....<<<<...<<<<.
..........>>>>..<<<<<...<<<<<<<....>>>>>>>......>>
.>>><<......>>.>>>><<<.....>>>..>>>>...<<<<<<.<<<<
<<<<..<<<<<<.>>>>>>.>>>.>>>>>>>>>>>......>>....>>.
..<<<<<<........>>>>>>....<<<<.<<<<......<<<<<<.<<
<<<<.<<<<<.<<<<<<<<<...<<<<<<<<<<.<<<<..........<<
<<<..<<<.>>>............>>>>>.>>>>.>>.>>>>>>>>..>>
>>>>>>>..>>>>>...<<<<<<<..<<<.........>>>>>>>>>>..
......>>>>>.>.>>>>>>.............<<<<<<...<..>...>
>>>>>.......((...<<<<<<<<<<<..<.<.<<<<<......>>>>>
...>.>.<<<.....))..>>>.....>>>>>....>>>>>>..<<<<<<
<....>>>.>>>>>>>>.>>>>..<<<<<<.<..<<<..<.<<<<<....
.............>>>>>.><<<<....<<<<.<<.<<<<<<<....>>>
>>..>>.>>...>>>>...>>>><<<<<...<<<<<...........>>>
>>...>>>>>.>>>...>.>>>>>>.<<<<<<<.<<..<<<<....<<<.
.......<<<<<.<<<<>>>>.>>>>>.......>>>...<<<..<<<<.
...<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>......
........>>>>..>>>>>>>>><<<<<.<.............>....<<
.<<<<<<<.<<.....<<<<....<<<<<......>>>>>...>>>>...
.>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkw Principles of human pre-60 S biogenesis.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): K7 L21 L23 S24 Q27 R28 T32 V33 I34 H35 H37 Y38 Q39 R49 K50 L66 K71 D90 K93 L94 L96 Q98 N100 I101 N104 L105 N108 Y124 K127 K130 R131 A132 G135 R136 T139 V140 R143 Q144 R155 R160 T163 R190 A191 Y198 F200 K203 H209 I236 R399
• Binding residue (residue number reindexed from 1): K6 L20 L22 S23 Q26 R27 T31 V32 I33 H34 H36 Y37 Q38 R48 K49 L65 K70 D89 K92 L93 L95 Q97 N99 I100 N103 L104 N107 Y123 K126 K129 R130 A131 G134 R135 T138 V139 R142 Q143 R154 R159 T162 R189 A190 Y197 F199 K202 H208 I235 R398

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