Structure of PDB 6hcf Chain D3 Binding Site BS01

Receptor Information

>6hcf Chain D3 (length=293) Species: 9986 (Oryctolagus cuniculus)

FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMI
VRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTG
LLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLAR
TTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQ
NVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPV
YEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAA

Ligand information

>6hcf Chain 52 (length=3634)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcgcgguccggccgugccggcggggcgg
aucucccgcucccgucggcgggggaccgccccccggccggcgaccggccg
ccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggac
ggcugggaaggccccggcggggaagguggcccgggggccccggguguuac
agccccgccccggcagcagcagcucgccgaaucccggggccgagggagcg
agacccgugcgccgcgcucuccccccucgggggggccgggccaccccucc
cacggcgcgaccgcucucccacccggggggcggggcggacuguccccagu
gcgccccgggcgggucgcgccgucgggcccgggggagguucucucggggc
cacgcgucccccgcgagcgcacggggucggcggcgaugucggcuacccac
ccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagucg
ggggcuacgaaagccgccguggcgcaaugaaggugaaggccggcggcgcg
ccgccggccgaggugggaucccgaggccuuccaguccgccgagggcgcac
caccggcccgucucgcccgccgcgccggggagguggagcacgagcgcacg
uguuaggacccgaaagauggugaacuaugccugggcagggcgaagccaga
ggaaacucugguggagguccguagcgguccugacgugcgaaucggucguc
cgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcugguu
cccuccaaaguuucccucaggauagcuggcgcucuccgcaguuuuauccg
guaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauuc
ucaaacuuuaaauggguaagaagcccggcucgcugguguggagccgggcg
uggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcug
cgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucag
accccagaaaagguguugguugauauagacagcaggaugguggccaugga
agucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacua
gcccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgc
uggcagucggcagagcgagaaagagaguggcgcggacgcuacgccgcgac
gaguaggagggccgcugcggugagccuugaagccuagggcgcgggcccgg
guggagccgccgcaggugcagaucuuggugguaguagcaaauauucaaac
gagaacuuugaaggccgaaguggagaaggguuccaugugaacagcaguug
aacaugggucagucgguccugagagaugggcgagcgccguuccgaaggga
cgggcgauggccuccguugcccucagccgaucgaaagggagucggguuca
gauccccgaauccggaguggcggagaugggcgccgcgaggcguccagugc
gguaacgcgaccgaucccggagaagccggcgggagccccggggagaguuc
ucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagag
aggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagc
ucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccgg
gccguacccauauccgcagcaggucuccaaggugaacagccucuggcaug
uuggaacaauguagguaagggaagucggcaagccggauccguaacuucgg
gauaaggauuggcucuaagggcuggcagccgacuuagaacuggugcggac
caggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcgg
cggguguugacgcgaugugauuucugcccagugcucugaaugucaaagug
aagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucucu
uaagguagccaaaugccucgucaucuaauuagugacgcgcaugaauggau
gaacgagauucccacugucccuaccuacuauccagcgaaaccacagccaa
gggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcuug
acucuagucuggcacggugaagagacaugagagguguagaauaaguggga
ggcccgggccgccggugaaauaccacuacucugaucguuuuuucacugac
ccggugaggcgggggggcgagccgggcucucgcuucuggcgccaagcgcc
cggccggccgggcgcgacccgcuccggggacagugccagguggggaguuu
gacuggggcgguacaccugucaaacgguaacgcagguguccuaaggcgag
cucagggaggacagaaaccucccguggagcagaagggcaaaagcucgcuu
gaucuugauuuucaguacgaauacagaccgugaaagcggggccucacgau
ccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccaca
gggauaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuug
auccuucgaugucggcucuuccuaucauugugaagcagaauucaccaagc
guuggauuguucacccacuaauagggaacgugagcuggguuuagaccguc
gugagacagguuaguuuuacccuacugaugauguguuguugccaugguaa
uccugcucaguacgagaggaaccgcagguucagacauuugguguaugugc
uuggcugaggagccaauggggcgaagcuaccaucugugggauuaugacug
aacgccucuaagucagaaucccgcccaggcggaacgauagcgccggagcc
ucgguuggccucggauagccggucccccgccgggguccggugcggagagc
ccuucgucccgggaaacggggcggccggaaagggggccgcccucucgccc
gucacgcaccgcacguucguggggaaccuggcgcuaaaccauucguagac
gaccugcuucugggucgggguuucguacguagcagagcagcugcugcgau
cuauugaaagucagcccucgacacaaggguuugu

.........................<<<<<<.....<......>......
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....>>>>.....((......<<<.....))>>>...>.>>>>>>>...>
>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>..
....((((..<<<<<<))))...]]]........................
..........<<....>>...............<<<......>>>.....
.............................<<<<<<<<..<<<.<....<<
<<<<<<.<<<.....<<<<<<<<<<.....<<<<<<.<<<<<.<<<<<<<
.<<<<<<<.<.......>>>>>>>>>>>>>>>>>>>>>>>>...>>..>>
>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<.<
<<<.........<..<<<<<<<......<<<<<<<...>>>>>>>.....
..>>>>>>>...>............>>>>...>>>>>>>>>>.....<<.
......>>.........<....<<<<<..>>>>>....<.<<..<<<.<<
<<<<<<<<<<<<<<<...<<.<<..>>>>.<<<<<<<...<<....>>..
.>>>>>>>>>>>.>>>>>>>>>>.>>>...>>>...<<....>>..>>.>
................>.........>>.>>>>>....>>>>...>>>>>
>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<..<<<.
..<<<.......>>>.....>>>...<<....>>...<<<<<<<<<<..>
>>>>>>>>>..<<<<<...<<<..<<<...(((.[[.>>>..>>>....>
>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>
>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<..<<<
<....>>>>..>.....>>>...<<<..<..<<........>>.>.>>>.
...>>>>>>>>>...<<.......>>......>>>>>>......>.>>..
<<<<<<....<.<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<<.
...<<<....<<<..<.<<<..<<<<.<.........>.>>>>>>>.>..
>>>...>>>....>>>>>>...<<<<<<<<<.<......>>>>>>>>>>.
...>>>>>>>>>>>>.>>>..<<<<.<<<<<.....>>>>>.>>>>....
<<<......>>>...<<<<<<<...<<<(((.......<<<<<.....<<
..........<<<.<<<<<<<<<........<..<........<<.....
....>>...............<<......>>.....>.>....>>>>>>>
>>>>>..........))).>>...>>>>>..>>>...>>>>>>><<<<<.
.<<<....................]].)))............>>>.>>>>
>....>>>>>>.<<<<<<<<<..<.......<<<<.<<<<....>>>>>>
>>....>.>>>>>>>.>>.....>>>>>><<<....<<.....<<<<<<.
......>>>>>>.<<<.....<<<<<.<<...<<<<<<...<<.....>>
.>>>>>>......<<<<<<...<<....<<<....>>>..........<.
.<<<<<.<<<...>>>.>>>>>.>......>>....>>>..<<<<<....
....>>>>>..<<<<....<<<.....<<<<<<<....>>>>>>>...<<
<....>>>......<<<<......<<<<<<<<<<<<<<<<<<<<<<...{
{{...>>>>>....<<<<<.<<<<.<<<<.....<<<.....>>>.....
>>>>>>>>..>>>>>.....<<<<<<<.......>>>>>>>>>>>.>.>>
>>>>>>>>>>............>>>>................>>>.>>>>
.>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>...
.<<<<.....<<<<<<<.<<.........<.....<<<<<....<<..>>
.....>>>>><<.<<<<<<<<<<<.>>>>>..>>>>>>.>>.........
...<<<<<<<<<..<<<.........>>>..<<<<<<<....<<<<....
.>>>>......>>>>>>>...<<..<<<..<<<<<<....<<<....<<<
<<....>>>>.>...>>>.>>>>..>>>>><<<<<<.......>>>>>>.
.......<...........<<<<<.......>>>>>.....>.....>>.
...>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>...>>>....<<<<
..........>>>>.....[[[[..{{{.{{......[[[[.{..[[[..
<<<<..<<<<<<<<......<<.<.<<<.<<<<..........<<<<<..
<<<<..>>>>............>>>>>.>>>>.>>.>>..>>.......<
<<<<.....<<<<..<<.<<.......>>>>..............<<<<<
<<<<..>>>>>>>>>..>>>>..>>>>>.....>>>>>>>>...>>>>..
..<<.....>>...<<<<<<...........>>>>>>..<<...<<<<<<
<...<<<<<<.......>>>>>>.....<<.[.(((>>....>>>>>>>.
..<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>)))].....
.((((((..(((..>>>>>>.)))))))))..........]]]....}]]
]].......<<..<<.<<<<<<...<<.......>>...>>>>>>...>>
.>.>.........<<<.<.<<<...<...<<<<<......>>>>>.....
>.<<<.........>>>......>>>...>...>>>.......<<<<<<<
....>>>.>>>>....}}..}}}.]]]]......<<<<<<....<<<..<
.<<<<<.................>>>>>.><<<<....<<<<....<<.<
<<<<<.}}}..>>>>..>>.>>...>>>>...>>>><<<<....<<<<..
...........>>>>....>>>>.>>>.....>>>>>>.<<<<<<<..<<
<.....<<<........<<<<<<..<<<<.>>>>>.>>>>>.......>>
>...<<<..<<<<....<<<<<<<<<........>>>>>>.>>>...>>>
>..>>>...............>>>..>.>>>>>>.<<<<<.<........
.....>....<<.<<<<<<<.<<.....<<<<.<..<<<<<.>>>>>..>
>>>>....>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hcf ZNF598 Is a Quality Control Sensor of Collided Ribosomes.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): F3 K5 K8 Y12 R15 Y16 K19 R23 D29 Y31 L36 K43 Y44 F113 P139 G140 Y145 L150 R152 K178 A274 D278 R279 Q282 S286
• Binding residue (residue number reindexed from 1): F1 K3 K6 Y10 R13 Y14 K17 R21 D27 Y29 L34 K41 Y42 F111 P137 G138 Y143 L148 R150 K176 A272 D276 R277 Q280 S284

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6hcf, PDBe:6hcf, PDBj:6hcf
• PDBsum: 6hcf
• PubMed: 30293783
• UniProt: P19949|RL5_RABIT Large ribosomal subunit protein uL18 (Gene Name=RPL5)