Structure of PDB 5jcs Chain s Binding Site BS01

Receptor Information

>5jcs Chain s (length=2003) Species: 559292 (Saccharomyces cerevisiae S288C)

TFVPTHKTVSSLRQLGRKIQNSTPIMLIGKAGSGKTFLINELSKYMGCHD
SIVKIHLGEQTDAKLLIGTYTSGDKPGTFEWRAGVLATAVKEGRWVLIED
IDKAPTDVLSILLSLLEKRELTIPSRGETVKAANGFQLISTVRINEDHQK
DSSNKIYNLNMIGMRIWNVIELEEPSEEDLTHILAQKFPILTNLIPKLID
SYKNVKSIYMNTKFISLNKGAHTRVVSVRDLIKLCERLDILFKNNGINKP
DQLIQSSVYDSIFSEAADCFAGAIGEFKALEPIIQAIGESLDIASSRISL
FLTQHVPTLENLDDSIKIGRAVLLKEKLNIQKKSMNSTLFAFTNHSLRLM
EQISVCIQMTEPVLLVGETGTGKTTVVQQLAKMLAKKLTVINVSQQTETG
DLLGGYKPKTVAVPIQENFETLFNATFSLKKNEKFHKMLHRCFNKNQWKN
VVKLWNEAYKMAQSILKITNTENENENAKKKKRRLNTHEKKLLLDKWADF
NDSVKKFEAQSSSIENSFVFNFVEGSLVKTIRAGEWLLLDEVNLATADTL
ESISDLLTEPDSRSILLSEKGDAEPIKAHPDFRIFACMNPATDVGKRDLP
MGIRSRFTEIYVHSPERDITDLLSIIDKYIGKYSVSDEWVGNDIAELYLE
AKKLSDNNTIVDGSNQKPHFSIRTLTRTLLYVTDIIHIYGLRRSLYDGFC
MSFLTLLDQKSEAILKPVIEKFTLGRLKNVKSIMSYIITPFVEKNMMNLV
RATSGKRFPVLIQGPTSSGKTSMIKYLADITGHKFVRINNHEHTDLQEYL
GTYVTDDTGKLSFKEGVLVEALRKGYWIVLDELNLAPTDVLEALNRLLDD
NRELFIPETQEVVHPHPDFLLFATQNPPGIYGGRKILSRAFRNRFLELHF
DDIPQDELEIILRERCQIAPSYAKKIVEVYRQLSIERSASRLFEQKNSFA
TLRDLFRWALRDAVGYEQLAASGYMLLAERCRTPQEKVTVKKTLEKVMKV
KLDMTKGMRRLSVLVSSCLKNKEPVLLVGETGCGKTTICQLLAQFMGREL
ITLNAHQNTETGDILGAQRPVRNRSEIQYKLIKSLKTALNIANDQDVDLK
ELLQLYSKSDNKNIAEDVQLEIQKLRDSLNVLFEWSDGPLIQAMRTGNFF
LLDEISLADDSVLERLNSVLEPERSLLLAEQGSSDSLVTASENFQFFATM
NPGGDYGKKELSPALRNRFTEIWVPSMEDFNDVNMIVSSRLLEDLKDLAN
PIVKFSEWFGKKLGGGNATSGVISLRDILAWVEFINKVFPKIQNKSTALI
QGASMVFIDALGTNNTAYLAENENDLKSLRTECIIQLLKLCGDDLNLTAP
TTASNLVRVVRAMQVHKPILLEGSPGVGKTSLITALANITGNKLTRINLS
EQTDLVDLFGADAPGERSGEFLWHDAPFLRAMKKGEWVLLDEMNLASQSV
LEGLNACLDHRGEAYIPELDISFSCHPNFLVFAAQNPQYQGGGRKGLPKS
FVNRFSVVFIDMLTSDDLLLIAKHLYPSIEPDIIAKMIKLMSTLEDQVCK
RKLWGNSGSPWEFNLRDTLRWLKLLNQYSICEDVDVFDFVDIIVKQRFRT
ISDKNKAQLLIEDIFPLECNVAVYESVLKAINNNWPLVLVGPSNSGKTET
IRFLASILGPRVDVFSMNSDIDSMDILGGYEQVDLTRQISYITEELTNIV
REIISMNMKLSPNATAIMEGLNLLKYLLNNIVTPEKFQDFRNRFNRFFSH
LEGHPLLKTMSMNIEKMTEIITKEASVKFEWFDGMLVKAVEKGHWLILDN
ANLCSPSVLDRLNSLLEIDGSLLINECSQEDGQPRVLKPHPNFRLFLTMD
PKYGELSRAMRNRGVEIYIDELHSRSTAFDRLTLGFELGENIDFVSIDDG
IKKIKLNEPDMSIPLKHYVPSYLSRPCIFAQVHDILLLSDEEPIEESLAA
VIPISHLGEVGKWANNVLNCTEYSEKKIAERLYVFITFLTDMGVLEKINN
LYK

Ligand information

>5jcs Chain x (length=3394)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugug
cccucugcuccuuguggguaggggaaucucgcauuucacugggccagcau
caguuuugguggcaggauaaauccauaggaauguagcuugccucgguaag
uauuauagccugugggaauacugccagcugggacugaggacugcgacgua
agucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgg
accaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgc
guaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgac
cgauccugaugucuucggauggauuugaguaagagcauagcuguugggac
ccgaaagauggugaacuaugccugaauagggugaagccagaggaaacucu
gguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggg
uauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaa
guuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcga
augauuagagguuccggggucgaaaugaccuugaccuauucucaaacuuu
aaauauguaagaaguccuuguuacuuaauugaacguggacauuugaauga
agagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaug
aaccgaacguagaguuaaggugccggaauacacgcucaucagacaccaca
aaagguguuaguucaucuagacagccggacgguggccauggaagucggaa
uccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaa
aauggauggcgcucaagcguguuaccuauacucuaccgucaggguugaua
ugaugcccugacgaguaggcaggcguggaggucagugacgaagccuagac
cguaaggucgggucgaacggccucuagugcagaucuuggugguaguagca
aauauucaaaugagaacuuugaagacugaaguggggaaagguuccacguc
aacagcaguuggacguggguuagucgauccuaagagauggggaagcuccg
uuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguua
agauuccggaaccuggauauggauucuucacgguaacguaacugaaugug
gagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcu
uaucaccccggaauugguuuauccggagauggggucuuauggcuggaaga
ggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauc
cacaggaaggaauaguuuucaugccaggucguacugauaaccgcagcagg
ucuccaaggugaacagccucuaguugauagaauaauguagauaagggaag
ucggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucg
gguagugagggccuuggucagacgcagcgggcgugcuuguggacugcuug
guggggcuugcucugcuaggcggacuacuugcgugccuuguuguagacgg
ccuugguaggucucuuguagaccgucgcuugcuacaauuaacgaucaacu
uagaacugguacggacaaggggaaucugacugucuaauuaaaacauagca
uugcgauggucagaaagugauguugacgcaaugugauuucugcccagugc
ucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcggga
guaacuaugacucucuuaagguagccaaaugccucgucaucuaauuagug
acgcgcaugaauggauuaacgagauucccacugucccuaucuacuaucua
gcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaa
gacccuguugagcuugacucuaguuugacauugugaagagacauagaggg
uguagaauaagugggagcuucggcgccagugaaauaccacuaccuuuaua
guuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacguuc
uagcauucaaggucccauucggggcugauccggguugaagacauugucag
guggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagaugu
ccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagggua
aaagcccccuugauuuugauuuucagugugaauacaaaccaugaaagugu
ggccuaucgauccuuuagucccucggaauuugaggcuagaggugccagaa
aaguuaccacagggauaacuggcuuguggcagucaagcguucauagcgac
auugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcaga
auucgguaagcguuggauuguucacccacuaauagggaacgugagcuggg
uuuagaccgucgugagacagguuaguuuuacccuacugaugaauguuacc
gcaauaguaauugaacuuaguacgagaggaacaguucauucggauaauug
guuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcugg
auuauggcugaacgccucuaagucagaauccaugcuagaacgcggugauu
ucuuugcuccacacaauauagauggauacgaauaaggcguccuuguggcg
ucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuug
ggugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuu
guauacgacuuagauguacaacgggguauuguaagcaguagaguagccuu
guuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jcs Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling
• Resolution: 9.5 Å
• Binding residue (original residue number in PDB): K1017 V1019 K1020
• Binding residue (residue number reindexed from 1): K728 V730 K731

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000055 ribosomal large subunit export from nucleus
• GO:0006364 rRNA processing
• GO:0110136 protein-RNA complex remodeling
• GO:2000200 regulation of ribosomal subunit export from nucleus

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005739 mitochondrion
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:5jcs, PDBe:5jcs, PDBj:5jcs
• PDBsum: 5jcs
• PubMed: 26619264
• UniProt: Q12019|MDN1_YEAST Midasin (Gene Name=MDN1)