Structure of PDB 6or5 Chain A Binding Site BS01

Receptor Information

>6or5 Chain A (length=2058) Species: 4896 (Schizosaccharomyces pombe)

DVLIEWVAIYPQIYDILEHINYVPSNTLQRLRLHQPWSKIDYDVWFLYAS
DEIRETCKVKYYGETKTYGEVFVLENERISQLHRLFVSERAEHLKNLLFD
ALPLVELGGNVFFNSHVPLPCSLVLTKSTQENLNRITPYLVQKRPILLAG
PEGIGKKFLITQIAAKLGQQIIRIHLSDSTDPKMLIGTYTWQPGVLTQAV
ITGWILFTNIEHEVLSVLLPLLEKRQLVIPSRGETIYAKGSFQMFATSSM
KTKILGQRLWQILDLTYQPDECVEVVSTLYPVLSIICPTLYSVYKDIFDL
FSSKIYRRLCLRDFYKFIKRVAFLYHKVFKEAIDMFGAFIPSRDGFDLVV
RNVAIELNIPPEKALQLPVFQNLEHNINIGRCSLKKLSTIRNSYAFTSSS
LGLLEQLAAGVQTNEPLLLVGETGTGKTTTIQLLAGLLGQKVTVINMSQQ
TESSDMLGSTLGLPLHERFIDIFEQTFSSKKNAKFISMASTSARRFRWKT
CLKIWKEACKLSKTVLNQVELRNQWAKFEKEVEDFEKVLTVEGALVKAVR
SGHWVLLDEINLASLETLEPIGQLLSPHKNFRLFGCMNPEPSFRSRFTEI
YVHSPDQNLDDLLSIIQKYIGSNEHVIREVAELYQVAKSLSLDPHYTVRT
LSRTLSYVTEIAPIYGLRRSLYEGFCMSFLTLLDHTSESLLYNHVVRFTL
NRDQQNAILKQIPKVPDYIAFCHYWLRRGPVEEQEHYIITPFVQKNLLNI
ARACSTRMPILIQGPTSSGKTSMIEYVAKKTGHKFVRINNHEHTDLQEYI
GTYVTDDNGSLSFREGVLVEALRNGYWIVLDELNLAPTDVLEALNRLLDD
NRELFIPQVLVKPHPEFMLFATQNPGRKHLSRAFRNRFLEIHFDDIPENE
LETILHKRCKIAPSYAAKIVQVFRELSLRRNSFATLRDLFRWAFREAVGY
QQLAENGYMLLAERARDQKDKLAVQEVIEKVMSKVVWTRPMIRLFCLVWR
CLLAKEPVLLVGDTGCGKTTVCQILAECLHKELHIINAHTENGDIIGAQR
PVRNRSAVNYSLHSQLCEKFNVIDDLIEKFEKLNLIERQIIKHDGALVTA
MKQFFLLDEISLADDSVLERLNSVLELSRTLTLAVSLTAKDGFAFFATMN
PGGKKELSPALRNRFTEIWVPTEDILKIVEGKLHNNKIELARPLVEYAKW
HANEYLYTDVISIRDVLSAVEFINACEILDLNLVLFNAVSMVFIDALLAS
LHAERQRCFAKLNELAHTDTTLMNASKVLRALQVLKPILLEGSPGVGKTS
LITALARETGHQLVRINLSDQTDLMDLFGSDVPVEAPFLAAMRNGHWVLL
DELNLASQSVLEGLNACLDHRNEAYIPELDKVFHPNFRVFAAQNPQGLPR
SFINRFSVVYVEALKEKDMIEIAACNYHQVNEDWRLKIIKFMFRLQDNIE
KDISGSPWEFNLRDTLRWLQLLNDAADYLEVMVLHRMRTVEDRVRTCELF
KEVFDIDYEPRTIGFSLSSQCFKVGHSLLVRDQKTLLDSQNILQSQLPVL
ESVITCINKKWPCILVGDTATGKTCILRLLAAIAGAKIKEMAVNSDTDTM
DLIDISRKASELFTDLSQQLLNIVIKYRNFDIFRETSLYTLTTSQAFTLL
QKVVDQLDETLVHSLGDIHEKARKLLAEFSASPAGGYLLKAVEEGHWFVL
DNANLCSPAVLDRLNSLLELIVNEKTTEDGHPKTIKPHPNFRLFLTVNPV
YGELSRAMRNRGVEIFLLKEALTEIDKKQMSLLEPAPISSAVDTLASNIS
YIKYVFETMGNYMYIAHAIILALFSPRQLKLLRKVLTLKNLVQKIYCADY
FNHMDLKASRFMDIYEYPVQLREVVGLIQTINDFQSVILTSHLELPETYA
SGLLFVSAHEILDLTEEVNTYLLKSASAVYGSTPSLWNLLNQFSKFLIEI
ASSNIVYKLDVIRHFLKLVVLWKNIYVWTSRFYCYTKMLGEWMFTKLLES
FLPKDSLEKFSELQTVESLRHYLESLYKESQILEIAESLNSGKVNSVMRR
LVSTEISN

Ligand information

• Ligand ID: ANP
• InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
• InChIKey: PVKSNHVPLWYQGJ-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
  ACDLabs 12.01: O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
• Formula: C10 H17 N6 O12 P3
• Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
• ChEMBL: CHEMBL1230989
• ZINC: ZINC000008660410
• PDB chain: 6or5 Chain A Residue 7201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6or5 Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): L132 V133 G162 G164
• Binding residue (residue number reindexed from 1): L123 V124 G153 G155
• Annotation score: 3

Gene Ontology

Molecular Function

• GO:0005509 calcium ion 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:0042254 ribosome biogenesis

Cellular Component

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

External links

• PDB: RCSB:6or5, PDBe:6or5, PDBj:6or5
• PDBsum: 6or5
• PubMed: 30318141
• UniProt: O94248|MDN1_SCHPO Midasin (Gene Name=mdn1)