Structure of PDB 8pqy Chain A Binding Site BS03

Receptor Information

>8pqy Chain A (length=2892) Species: 9606 (Homo sapiens)

AIVKDVLLVAQGEMALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDL
FNKVKEHINSVSAMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRR
WVYLEGIFTGSADIKHLLPVETQEFQSISTEFLALMKKVSKSPLVMDVLN
IQGVQRSLERLADLLGEIQKALGEYLERERSSFPRFYFVGDEDLLEIIGN
SKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSREGEEVMFKTPVSIT
EHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYITWID
KYQAQLVVLSAQIAWSENVETALSSAAPLHSVLSNVEVTLNVLADSVLME
QPPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPK
QTDVLQQLSIQMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEAR
LGGSPFGPAGTGKTESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLC
QVGAWGCFDEFNRLEERMLSAVSQQVQCIQEALREHSNPITCELLNKQVK
VSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQ
GFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRER
IQKIKREAENLPEQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGVQY
HRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGL
MMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDP
NTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLD
DNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDVLS
TDMIFNNFLARLRSIPLDEASPMLQIQRDAATIMQPYFTSNGLVTKALEH
AFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQYNANHPDFPMQIEQLERY
IQRYLVYAILWSLSGDSRLKMRAELGEYIRRITTVPLPTAPNIPIIDYEV
SISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEALLYTWLAEHK
PLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHYC
EYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEH
GGFYRTSDQTWVKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYP
GPASLTQIYGTFNRAMLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQDTQ
PHYIYSPREMTRWVRGIFEALRPLETLPVEGLIRIWAHEALRLFQDRLVE
DEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLSKDYIPVDQEEL
RDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVS
GAGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEK
IAFIMDESNVLDSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQK
EGLMLDSHEELYKWFTSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNRC
VLNWFGDWSTEALYQVGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPSH
REAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFINHYANLFHE
KRSELEEQQMHLNVGLRKIKETVDQVEELRRDLRIKSQELEVKNAAANDK
LEYAVLISEAQAIKADLAAVEAKVNRSTALLKSLSAERERWEKTSETFKN
QMSTIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIA
RTEYLSNADERLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATE
FIMNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPV
LNREVRRTGGRVLITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTF
VNFTVTRSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKS
LLQALNEVKGRILDDDTIITTLENLKREAAEVTRKVEETDIVMQEVETVS
QQYLPLSTACSSIYFTMESLKQIHFLYQYSLQFFLDIYHNVLYENPNLVT
DHTQRLSIITKDLFQVAFNRVARGMLHQDHITFAMLLARIKLKGTGEPTY
DAEFQHFLRGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKV
QADEQFGIWLDSSSPEQTVPYLWTPATPIGQAIHRLLLIQAFRPDRLLAM
AHMFVSTNLGESFMSIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGH
VEDLAAEQNTQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLAPG
WLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVK
ANMLRTFSSIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKK
YEFGESDLRSACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGG
RVDNEFDQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREE
FVQWVELLPDTQTPSWLGLPNNAERVLLTTQGVDMISKMLKMQMLETLHT
TASNWLHLIPQTLSHLKRTENIKDPLFRFFEREVKMGAKLLQDVRQDLAD
VVQVCEGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSDFS
ERIKQLQNISLAAASKELKNIHVCLGGLFVPEAYITATRQYVAQANSWSL
EELCLEVNVSFGVTGLKLQGATCNNNKLSLSNAISTALPLTQLRWVKQSV
VTLPVYLNFTRADLIFTVDFEIATKEDPRSFYERGVAVLCTE

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 8pqy Chain A Residue 4803

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pqy Molecular mechanism of dynein-dynactin complex assembly by LIS1
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): L2191 W2203 S2226 S2228 G2229 K2230 S2231 M2232 E2344 L2369 M2373 N2377 R2684 R2726 R2729
• Binding residue (residue number reindexed from 1): L721 W733 S756 S758 G759 K760 S761 M762 E874 L899 M903 N907 R1195 R1237 R1240
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008569 minus-end-directed microtubule motor activity
• GO:0016887 ATP hydrolysis activity
• GO:0045505 dynein intermediate chain binding
• GO:0051959 dynein light intermediate chain binding

Biological Process

• GO:0007018 microtubule-based movement
• GO:0007052 mitotic spindle organization
• GO:0007097 nuclear migration
• GO:0008090 retrograde axonal transport
• GO:0031122 cytoplasmic microtubule organization
• GO:0032388 positive regulation of intracellular transport
• GO:0033962 P-body assembly
• GO:0034063 stress granule assembly
• GO:0051293 establishment of spindle localization
• GO:0051301 cell division
• GO:0060236 regulation of mitotic spindle organization
• GO:0090235 regulation of metaphase plate congression
• GO:0120162 positive regulation of cold-induced thermogenesis
• GO:1905832 positive regulation of spindle assembly

Cellular Component

• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0005813 centrosome
• GO:0005829 cytosol
• GO:0005856 cytoskeleton
• GO:0005868 cytoplasmic dynein complex
• GO:0005874 microtubule
• GO:0005881 cytoplasmic microtubule
• GO:0005938 cell cortex
• GO:0016020 membrane
• GO:0030175 filopodium
• GO:0030286 dynein complex
• GO:0035578 azurophil granule lumen
• GO:0070062 extracellular exosome
• GO:1904115 axon cytoplasm

External links

• PDB: RCSB:8pqy, PDBe:8pqy, PDBj:8pqy
• PDBsum: 8pqy
• PubMed: 38547289
• UniProt: Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)