Structure of PDB 8esr Chain v Binding Site BS01

Receptor Information

>8esr Chain v (length=161) Species: 4896 (Schizosaccharomyces pombe)

ANPRQRNKQRSGKPRLTRRNANKKAKAKIYGNFVIQQNWDKHATLRQNYA
RLGLLATPNYVTGGVEKLYPDPTLDDVLDKEISIAPAKTEVVRQLEEEAV
KKAARQSNKMLPLSAFEHAYIQRLINKYGTEDFESMAKDVKLNSKLFNGS
KLKNLYIRMKA

Ligand information

>8esr Chain 1 (length=2143)

uugaccucaaaucagguaggacuacgcgcugaacaauaagcgcaggaaaa
gaaaauaaccaugauucccucaguaacggugaagcgggaaaagcucaaau
uugaaaucuggcaacauuucuuuuguuguccgaguuguaauuucaagaag
cugcuuugaguguagacgaucggucuaaguuccuuggaacaggacgucag
agagggugagaaccccgucuuuggucgauuggauaugccauauaaagcgc
uuucgaagagucgaguugugcagcucuaaaugggugguucaucuaaagcu
aaauauuggcgagagaccgauagcgaacaaguagagugaucgaaagauga
aaagaacuuugaaaagagaguuaaauaguacgugaaauugcugaaaggga
agcauuggaaaucaggucagcaucaguuuucgggggcggaaaaagaauaa
gggaagguggcuguuuauagcccuuguuguaauacguccacuggggacug
aggacugcggcuugccaaggaugcugacauaaugguuuucaauggcccgu
cuugaaacacggaccaaggagucuagcaucuaugcgaguguuugggugau
gaaaacccauccgcgaaauggugaaugcaggugggaacgcccuggcgugc
accaucgaccguaagagcauagcuguugggacccgaaagauggugaacua
ugccugaauuggguauaggaaccaucuaguagcugguuccugccgaaguu
uccggauagcagaaacucagaucaguuuuauguguaaaaugagaguuucu
agugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacg
ugagguuaaggugccggaauguacgcucaucagagaaaagguguuaguuc
aucuagacagcaggacgguggccauggaagucggaauccgcuaaggagug
uguaacaacucaccugccgaaugaacuagcccugaaaauggauggcgcuu
aagcguacuacccauaccucaccgucuggguuagagaagcucagacgagu
aggcaggcguggagguuugugacgaagccuugggcgugagccugggucga
acagccucuagugcagaucuugguggaaguagcauucaaaugagaacuuu
gaagacugaaguggggaaagguuccaugugaacagcaguuggacaugggu
uagucgauccuaagagauagggaagcuccguaugaaaguugcacgauuuu
ucgugccuaucgaaagggaauccgguuaauauuccggaaccagaaggugg
aaucacggcaacguaaaugaaguuggagacgucggcgggagcccugggaa
gaguucucuuuucuuuuuaacaaaccacacccugaaaucgguuuauccgg
agcuaggguaugguguuuggaagaguucagcggcugaauccggugcgcuc
ucgacggcccuugaaaauccaacggaagguuuucacaucuggucguacuc
cuccaaggugccucuaguugauagaacaauguagauaagggaagucggca
aaaugggcccacugucccuaucuacuaucuagcgaaaccacagccugggg
aacgggccaggcaaaaucagcggcccuguugagcuugacucuaguuugca
gguggggaguuaaaguuaccacagggaucuuguggcagccaagcgcgacg
uugcuucggcucuuccuaucauaccgaagcagaauucgguaagcguugga
cccacuaauagggaacgugagcugggaccgucgugagacgguuagucuac
ugaugaagugucgucgcaaugguaauucaacuuaguacgagaggaaccgu
ugauucagaucauugguauuugcggcugccugacaaggcaaugccgcgga
gcuaucaucugccggauaacggcugaacgccucuaagccagaauccgugc
cagaaagcgacgauauguauaaaaauagagguaggcuacucuccuguauc
guagaagaugggcgaugguugaugaaacggaaguguuuuauugacuuguc
caugaaauuccaugaauccauugcauacgacuuuaauguggaacggggua
uuguaagcagcugcugagauuaagccuuuguucccaagauuug

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8esr Chromatin localization of nucleophosmin organizes ribosome biogenesis.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): A2 N3 R5 Q6 R7 K9 R11 R16 L17 T18 R19 R20 K25 K29 I30 Q37 K42 H43 T45 R47 Y61 T63 G64 G65 E67 K155 S160 F162 E163 K191 N194 S196
• Binding residue (residue number reindexed from 1): A1 N2 R4 Q5 R6 K8 R10 R15 L16 T17 R18 R19 K24 K28 I29 Q36 K41 H42 T44 R46 Y60 T62 G63 G64 E66 K109 S114 F116 E117 K145 N148 S150

Gene Ontology

Molecular Function

• GO:0003674 molecular_function

Biological Process

• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8esr, PDBe:8esr, PDBj:8esr
• PDBsum: 8esr
• PubMed: 36423630
• UniProt: Q9Y7Z1|NOP16_SCHPO Nucleolar protein 16 (Gene Name=nop16)