Structure of PDB 6hyp Chain A Binding Site BS02

Receptor Information
>6hyp Chain A (length=2272) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAPSVPECFTIE
KKSSYFIIEPQDLSTKVASICGVIVPKVHTIHDKVFYPLTFVPTHKTVSS
LRQLGRKIQNSTPIMLIGKAGSGKTFLINELSKYMGCHDSIVKIHLGEQT
DAKLLIGTYTSFEWRAGVLATAVKEGRWVLIEDIDKAPTDVLSILLSLLE
KRELTIPSRGETVKAANGFQLISTVRNLNMIGMRIWNVIELEEPSEEDLT
HILAQKFPILTNLIPKLIDSYKNVKSIYMNTKFISLNKGAHTRVVSVRDL
IKLCERLDILFKNNGINKPDQLIQSSVYDSIFSEAADCFAGAIGEFKALE
PIIQAIGESLTQHVPTLENLDDSIKIGRAVLMNSTLFAFTNHSLRLMEQI
SVCIQMTEPVLLVGETGTGKTTVVQQLAKMLAKKLTVINVSQQTETGDLL
GGYKPVNSKTVAVPIQENFETLFNATFSLKKNEKFHKMLHRCFNKNQWKN
VVKLWNEAYKLLDKWADFNDSVKKFEAQSSSIENSFVFNFVEGSLVKTIR
AGEWLLLDEVNLATADTLESISDLLTEPDSRSILLSAEPIKAHPDFRIFA
CMNPATDVGKRDLPMGIRSRFTEIYVHSPERDITDLLSIIDKYIGKYSVS
DEWVGNDIAELYLEAKKLSDNNTIVDGSNQKPHFSIRTLTRTLLYVTDII
HIYGLRRSLYDGFCMSFLTLLDQKSEAILKPVIEKFTLGRLKNVKSIMSQ
TPPSPGPDYQAHYIITPFVEKNMMNLVRATSGKRFPVLIQGPTSSGKTSM
IKYLADITGHKFVRINNHEHTDLQEYLGTYVTDDTGKLSFKEGVLVEALR
KGYWIVLDELNLAPTDVLEALNRLLDDNRELFIPETQEVVHPHPDFLLFA
TQNPPGIYGGRKILSRAFRNRFLELHFDDIPQDELEIILRERCQIAPSYA
KKIVERLFEQKNSFATLRDLFRWAVGYEQLAASGYMLLAERCRTPQEKVT
VKKTLEKVMKLEAIGSVTWTKGMRRLSVLVSSCLKNKEPVLLVGETGCGK
TTICQLLAQFMGRELITLNAHQNTETGDILGAQEWSDGPLIQAMRTGNFF
LLDEISLADDSVLERLNSVLEPERSLLLAESDSLVTASENFQFFATMNPG
GDYGKKELSPALRNRFTEIWVPSMEDFNDVNMIVSSRLLEDLKDLANPIV
KFSEWFGKNATSGVISLRDILAWVEFINKVFPKIQNKSTALIQGASMVFI
DALGTNNTAYLAENENDLKSLFNLTAPTTASNLVRVVRAMQVHKPILLEG
SPGVGKTSLITALANITGNKLTRINLSEQTDLVDLFGAHDAPFLRAMKKG
EWVLLDEMNLASQSVLEGLNACLDHRGEAYIISFSCHPNFLVFAAQNPKG
LPKSFVNRFSVVFIDMLTSDDLLLIAKHLYPSIEPDIIAKMIKLMSTLED
QVCKRKLWGNSGSPWEFNLRDTLRWLKLLNQYSICEDVDVFDFVDIIVKQ
RFRTISDKNKAQLLIEDIFGKFSTKENFFKLTEDYVQINNEVALRNPHYR
YPITQNLFPLECNVAVYESVLKAINNNWPLVLVGPSNSGKTETIRFLASI
LGPRVDVFSMNSDIDSMDILGGYEQVDLTRQISYITEELTNIVREIISMN
MKLSPNATAIMEGLNLLKYLLNNIVTPEKFQDFRNRFNRFFSHLEGHPLL
KTMSMNIEKMTEIITKEASVKFEWFDGMLVKAVEKGHWLILDNANLCSPS
VLDRLNSLLEIDGSLLIQPRVLKPHPNFRLFLTMDPKYGELSRAMRNRGV
EIYIDELHSRSTAFDRLTLGFPDMSIPLKHYVPSYLSRPCIFAQVHDILL
LSDEEPIEESLAAVIPISHLGEVGKWANNVLNCTEYSEKKIAERLYVFIT
FLTDMGVLEKINNLYKPANLKFQKALGLHDKQLTEETVSLTLNEYVLPTV
SKYSDKIKSPESLYLLSSLRLLLNSLNALKLINEKSTHGKIDELTYIELS
AAAFIFCILYNILTVMSENLKTESLFCGSNQYQYYWDLLVIVIAALETAV
TKDEARLRVYKELIDSWIASVKSKSDAIHDYVLYDLFLKTKTFSQNLMKS
WRNVRKVISGDEEIFTEKLINT
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6hyp Chain A Residue 5002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6hyp The CryoEM structure of the Saccharomyces cerevisiae ribosome maturation factor Rea1.
Resolution4.4 Å
Binding residue
(original residue number in PDB)		F2028 N2057 S2058 G2059 K2060 T2061 E2062
Binding residue
(residue number reindexed from 1)		F1708 N1737 S1738 G1739 K1740 T1741 E1742
Annotation score5
Enzymatic activity
Enzyme Commision number ?
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6hyp, PDBe:6hyp, PDBj:6hyp
PDBsum6hyp
PubMed30460895
UniProtQ12019|MDN1_YEAST Midasin (Gene Name=MDN1)

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