Structure of PDB 8fl4 Chain NP Binding Site BS01

Receptor Information

>8fl4 Chain NP (length=104) Species: 9606 (Homo sapiens)

RSRRTGAHRAHSLARQMKAKRRRPDLDEIHRELRFDPDLPGGGLHRCLAC
ARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERAAGMGSYVPPRR
LAVP

Ligand information

>8fl4 Chain L3 (length=3486)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggauucaacccggcggcggccggccgugucggcggcccggcggaucug
ggaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgc
ggcggugcgccgcgaccggcuccgggacggcugggaaggcccggcgggga
agguggcucgggcccgaguguuacagcccccccggcagcagcacucgccg
aaucccggggccgagggagucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgcgccgucgggcccggggggccacgcgcgcgucc
cccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucg
gcuacccacccgacccgucuugaaacacggaccaaggagucuaacacgug
cgcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaag
gccgcggccgaggugggaucccgaggcccgccgagggcgcaccaccggcc
cgucucgcccgccgcgccggggagguggagcacgagcgcacguguuagga
cccgaaagauggugaacuaugccugggcagggcgaagccagaggaaacuc
ugguggagguccguagcgguccugacgugcaaaucggucguccgaccugg
guauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccga
aguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaagcg
aaugauuagaggucuuggggccggaucucaaccuauucucggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguu
aaggcgcccgaugccgacgcucaucagaccccagaaaagguguugguuga
uauagacagcaggacgguggccauggaagucggaauccgcuaaggagugu
guaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugg
agcgucgggcccauacccggccgucgccggcagugacgcuacgccgcgac
gaguaggagggccgcugcggugagccuugaagccuagggcgcgggcccgg
guggagccgccgcaggugcagaucuuggugguaguagcaaauauucaaac
gagaacuuugaaggccgaaguggagaaggguuccaugugaacagcaguug
aacaugggucagucgguccugagagaugggcgagcgccguuccgaaggga
cgggcgaugcccucgaucgaaagggagucggguucagauccccgaauccg
gaguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccga
ucccggagaagccggcgggagccccggggagaguucucuuuucuuuguga
agggcagggcgcccuggaauggguucgccccgagagaggggcccgugccu
uggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuu
gaaaauccgggggagaggguguaaaucucgcgccgggccguacccauauc
cgcagcaggucuccaaggugaacagccucuggcauguuggaacaauguag
guaagggaagucggcaagccggauccguaacuucgggauaaggauuggcu
cuaagggcugggucggucgggcuggggcgcgaagcggggucccguggauc
gccccagccggccggcgccuagcagccgacuuagaacuggugcggaccag
gggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccggggugu
ugacgcgaugugauuucugcccagugcucugaaugucaaagugaagaaau
ucaaugaagcgcggguaaacggcgggaguaacuaugacucucuuaaggua
gccaaaugccucgucaugugacgcgcaugaauggaugaacgagauuccca
cugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuugg
cggaaucagcggggaaagaagacccuguugagcuugacucuagucuggca
cggugaagagacaugagagguguagaauaagugggaggcggccgccggug
aaauaccacuacucugaucguuuuuucacugacccggugaggcggggggc
uucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccg
gggacagugccagguggggaguuugguacaccugucaaacgguaacgcag
guguccuaaggcgagcucagggaggacagaaaccucccguggagcagaag
ggcaaaagcucgcuugaucuugauuuuguacgaauacagaccgugaaagc
ggggccucacccuucugaccuuuuggguuuuaagcaggaggaaguuacca
cagggauaacuggcuuguggcggccaagcgagcgacgucgcuuuuugauc
cuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugauguguuguugccaugguaaucc
ugcucaguacgagaggaaccgcagguucagacauuugguguaugugcuug
gcugaggagccaauggggcgaagcuaccaucugugggauuaugacugaac
gccucuaagucagaaucccgcccaggcggaacgauagcgccgcggagccu
cgguuggccucggauagccgguccccgggguccggugcggagugcccuuc
guccugggaaacggggcgcggccggagaggcggccgcccccucgcccguc
acgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgac
cugcuucugggucgggguuucguacguagcagagcagcucccucgcugcg
aucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fl4 Principles of human pre-60 S biogenesis.
• Resolution: 2.89 Å
• Binding residue (original residue number in PDB): R3 S4 R5 R6 T7 H10 R11 A12 H13 S14 L15 R17 K20 A21 R23 R68 N75 R81 K83 D84 K86 K87 R88 K90
• Binding residue (residue number reindexed from 1): R1 S2 R3 R4 T5 H8 R9 A10 H11 S12 L13 R15 K18 A19 R21 R52 N59 R65 K67 D68 K70 K71 R72 K74

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding
• GO:1990275 preribosome binding

Biological Process

• GO:0042254 ribosome biogenesis
• GO:0045944 positive regulation of transcription by RNA polymerase II
• GO:1903026 negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm

External links

• PDB: RCSB:8fl4, PDBe:8fl4, PDBj:8fl4
• PDBsum: 8fl4
• PubMed: 37410842
• UniProt: O00488|ZN593_HUMAN Zinc finger protein 593 (Gene Name=ZNF593)