Structure of PDB 8fld Chain NP Binding Site BS01

Receptor Information

>8fld Chain NP (length=108) Species: 9606 (Homo sapiens)

RSRRTGAHRAHSLARQMKAKRRRPDLDEIHRELRFDPDLPGGGLHRCLAC
ARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERAAGMGSYVPPRR
LAVPTEVS

Ligand information

>8fld Chain L3 (length=3372)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccggggcgcgggacauguggc
guacggaagacccgcuccccggcgccgcgggggcccaaguccuucugauc
gaggcccagcccguggacggugugaggccgguagcggcccccggcgcgcc
gggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcg
ggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaa
caaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaaga
gggcgugaaaccguuaagaggaacgggugggguccgcgcaguccgcccgg
aggauucaacccggcggcggccggccgugucggcggcccggcggaucugg
gaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgcg
gcggugcgccgcgaccggcuccgggacggcugggaaggcccggcggggaa
gguggcucgggcccgaguguuacagcccccccggcagcagcacucgccga
aucccggggccgagggaggucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgaccgcucggggcggacuguccccagugcgcccc
gggcgggucgcgccgucgggcccggggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgcgg
ccgaggugggaucccgaggccucuccaguccgccgagggcgcaccaccgg
cccgucucgcccgccgcgccggggagguggagcacgagcgcacguguuag
gacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaac
ucugguggagguccguagcgguccugacgugcaaaucggucguccgaccu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccucc
gaaguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaag
cgaaugauuagagguaccuauucucaaacuuuaaauggguaagaagcccg
gcucgcuggcguggagccgggcguggaaugcgagugccuagugggccacu
uuugcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgccc
gaugccgacgcucaucagaccccaaaagguguugguugauauagacagca
ggacgguccgcuaagaccugccgaaucaacuagcccugaaaauggauggc
gcuggagcgucgggcccauacccggccgucgccggcagucgagaguggac
gggagcggcgcgcggacgcuacgccgcgacgaguaggagggccgcugcgg
ugagccuugaagccuagggcgcgggcccggguggagccgccgcaggugca
gaucuuggugguaguagcaaauauucaaacgagaacuuugaaggccgaag
uggagaaggguuccaugugaacagcaguugaacaugggucagucgguccu
gagagaugggcgagcgccguuccgaagggacgggcgauggccuccggccc
ugaucgaaagggagucggguucagauccccgaauccggaguggcggagau
gggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaagcc
ggcgggagccccggggagaguucucuuuucuuugugaagggcagggcgcc
cuggaauggguucgccccgagagaggggcccgugccuuggaaagcgucgc
gguuccggcggcguccggugagcucucgcuggcccuugaaaauccggggg
agaggguguaaaucucgcgccgggccguacccauauccgcagcaggucuc
caaggugaacagccucuggcauguuggaacaauguagguaagggaagucg
gcaagccggauccguaacuucgggauaaggauuggcucuaagggcugggu
cggucgggcuggggcgcgaagcggggucccguggaucgccccagccggcc
ggcgccuagcagccgacuuagaacuggugcggaccaggggaauccgacug
uuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcgau
gugauuucugcccagugcucugaaugucaaagugaagaaauucaaugaag
cgcggguaaacggcaagugaacgagauucccacugucccuaccuacuauc
cagcgaaaccacagccaaggcgggcuuggcggaaucagcggggaaagaag
acccuguugagcuugacucuagucuggcacggugaaguuuuuucacugac
ccggugaggcggggggcuucuggcgccaagcgcccggccgcgcgccggcc
gggcgcgacccgcuccggggacagugccagguggggaguuugacuguaca
ccugucaaacgguaacgcagguguccuaaggcgagcucagggaggacaga
aaccucccguggagcagaagggcaaaagcucgcuugaucuugauuuucag
uacgaauacagaccgugaaagcggggccucacgauccuucugaccuuuug
gguuuuaagcaggaggugucagaaaaguuaccacagggaugaugucggcu
cuuccuaucauugugaagcagaauucaccaagcguuggauuguucaccca
cuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuu
uacccuacugaugauguguuguugccaugguaauccugcucaguacgaga
ggaaccgcagguucagacauuugguguaugugcuuggcugaggagccaau
ggggcgaagcuaccaucugugggauuaugacugaacgccucuaagucaga
aucccgcccaggcggaacgauagcgccgcggagccucgguuggccucgga
uagccgguccccgggguccggugcggagugcccuucguccugggaaacgg
ggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguu
cguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucg
ggguuucguacguagcagagcagcucccucgcugcgaucuauugaaaguc
agcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fld Principles of human pre-60S biogenesis
• Resolution: 2.58 Å
• Binding residue (original residue number in PDB): R3 S4 R5 R6 T7 G8 A9 H10 R11 A12 H13 L15 R17 K20 A21 R23 R68 I71 N75 K83 D84 K87 Q91
• Binding residue (residue number reindexed from 1): R1 S2 R3 R4 T5 G6 A7 H8 R9 A10 H11 L13 R15 K18 A19 R21 R52 I55 N59 K67 D68 K71 Q75

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