Structure of PDB 7z8f Chain m Binding Site BS01

Receptor Information

>7z8f Chain m (length=4562) Species: 9606 (Homo sapiens)

AVQNVADVSVLQKHLRKLVPLLLEDGGEAPAALEAALEEKSALEQMRKFL
SDPQVHTVLVERSTLKEDVGDEGEEEKEFISYNINIDIHYGVKSNSLAFI
KRTPVIDADKPVSSQLRVLTLSEDSPYETLHSFISNAVAPFFKSYIRESG
KADRDGDKMAPSVEKKIAELEMGLLHLQQNIEIPEISLPIHPMITNVAKQ
CYERGEKPKVTDFGDKVEDPTFLNQLQSGVNRWIREIQKVTKLDRDPASG
TALQEISFWLNLERALYRIQEKRESPEVLLTLDILKHGKRFHATVSFDTD
TGLKQALETVNDYNPLMKDFPLNDLLSATELDKIRQALVAIFTHLRKIRN
TKYPIQRALRLVEAISRDLSSQLLKVLGTRKLMHVAYEEFEKVMVACFEV
FQTWDDEYEKLQVLLRDIVKRKREENLKMVWRINPAHRKLQARLDQMRKF
RRQHEQLRAVIVRVLRDAADANAIEEVNLAYENVKEVDGLDVSKEGTEAW
EAAMKRYDERIDRVETRITARLRDQLGTAKNANEMFRIFSRFNALFVRPH
IRGAIREYQTQLIQRVKDDIESLHDKFKVQYPQSQACKMSHVRDLPPVSG
SIIWAKQIDRQLTAYMKRVEDVLGKGWENHVEGQKLKQDGDSFRMKLNTQ
EIFDDWARKVQQRNLGVSGRIFTIKLKVNFLPEIITLSKEVRNLKWLGFR
VPLAIVNKAHQANQLYPFAISLIESVRTYERTCEKVEERNTISLLVAGLK
KEVQALIAEGIALVWESYKLDPYVQRLAETVFNFQEKVDDLLIIEEKIDL
EVRSLETCMYDHKTFSEILNRVQKAVDDLNLHSYSNLPIWVNKLDMEIER
ILGVRLQAGLRAWTQVLLGQAEDKAEVDMDTDAPQVSHKPGGEPKIKNVV
HELRITNQVIYLNPPIEECRYKLYQEMFAWKMVVLSLPRIQSQRYQVGVH
YELTEEEKFYRNALTRMPDGPVALEESYSAVMGIVSEVEQYVKVWLQYQC
LWDMQAENIYNRLGEDLNKWQALLVQIRKARGTFDNAETKKEFGPVVIDY
GKVQSKVNLKYDSWHKEVLSKFGQMLGSNMTEFHSQISKSRQELEQHSVD
TASTSDAVTFITYVQSLKRKIKQFEKQVELYRNGQRLLEKQRFQFPPSWL
YIDNIEGEWGAFNDIMRRKDSAIQQQVANLQMKIVQEDRAVESRTTDLLT
DWEKTKPVTGNLRPEEALQALTIYEGKFGRLKDDREKCAKAKEALELTDT
GLLSGSEERVQVALEELQDLKGVWSELSKVWEQIDQMKEQPWVSVQPRKL
RQNLDALLNQLKSFPARLRQYASYEFVQRLLKGYMKINMLVIELKSEALK
DRHWKQLMKRLHVNWVVSELTLGQIWDVDLQKNEAIVKDVLLVAQGEMAL
EEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVKEHINSVSAMKL
SPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSADIKH
LLPVETQEFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLG
EIQKALGEYLERERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFA
GVSSIILNEDNSVVLGISSREGEEVMFKTPVSITEHPKINEWLTLVEKEM
RVTLAKLLAESVTEVEIFGKATSIDPNTYITWIDKYQAQLVVLSAQIAWS
ENVETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQPPLRRRKLE
HLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSI
QMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAG
TGKTESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDE
FNRLEERMLSAVSQQVQCIQEALREHSNPNYDKTSAPITCELLNKQVKVS
PDMAIFITMNPGSNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQGFRTAE
VLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRERIQKIKR
EKEERGEAVDEGEIAENLPEQEILIQSVCETMVPKLVAEDIPLLFSLLSD
VFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQI
TQINHGLMMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDH
LYGTLDPNTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVE
NLNSVLDDNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRCGMVW
FSEDVLSTDMIFNNFLARLRSIPLDEGEDEAQRRRKGKEDEGEEAASPML
QIQRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSLFSMLH
QACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLKMRAE
LGEYIRRITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVETHKVA
APDVVVPTLDTVRHEALLYTWLAEHKPLVLCGPPGSGKTMTLFSALRALP
DMEVVGLNFSSATTPELLLKTFDHYCEYRRTPNGVVLAPVQLGKWLVLFC
DEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQTWVKLERIQFVGACN
PPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRLIPSLR
TYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEALRPL
ETLPVEGLIRIWAHEALRLFQDRLVEDEERRWTDENIDTVALKHFPNIDR
EKAMSRPILYSNWLSKDYIPVDQEELRDYVKARLKVFYEEELDVPLVLFN
EVLDHVLRIDRIFRQPQGHLLLIGVSGAGKTTLSRFVAWMNGLSVYQIKV
HRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNVLDSGFLERMNTLLA
NGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWFTSQVIRNLH
VVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALYQVGKEFTSKM
DLEKPNYIVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTLHQANARLAK
RGGRTMAITPRHYLDFINHYANLFHEKRSELEEQQMHLNVGLRKIKETVD
QVEELRRDLRIKSQELEVKNAAANDKLKKMVKDQQEAEKKKVMSQEIQEQ
LHKQQEVIADKQMSVKEDLDKVEPAVIEAQNAVKSIKKQHLVEVRSMANP
PAAVKLALESICLLLGESTTDWKQIRSIIMRENFIPTIVNFSAEEISDAI
REKMKKNYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYADMLKRVEPLR
NELQKLEDDAKDNQQKANEVEQMIRDLEASIARYKEEYAVLISEAQAIKA
DLAAVEAKVNRSTALLKSLSAERERWEKTSETFKNQMSTIAGDCLLSAAF
IAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADERLRWQ
ASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEYKDRKITRTS
FLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRVLIT
LGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCL
NEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDD
DTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQQYLPLSTACSSIYF
TMESLKQIHFLYQYSLQFFLDIYHNVLYENPNLKGVTDHTQRLSIITKDL
FQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPTYDAEFQHFLRGNE
IVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDS
SSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNL
GESFMSIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQN
TQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKL
HSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFSS
IPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLR
SACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQR
LLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLP
DTQTPSWLGLPNNAERVLLTTQGVDMISKMLKMQMLEDEDAWMRTLHTTA
SNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKLLQDVRQDLADV
VQVCEGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSDFSE
RIKQLQNISLAAASGGAKELKNIHVCLGGLFVPEAYITATRQYVAQANSW
SLEELCLEVNVTTSQGATLDACSFGVTGLKLQGATCNNNKLSLSNAISTA
LPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIFTVDFEIATKEDPRS
FYERGVAVLCTE

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 7z8f Chain m Residue 4701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7z8f Structure of dynein-dynactin on microtubules shows tandem adaptor binding.
• Resolution: 20.0 Å
• Binding residue (original residue number in PDB): V1880 G1909 T1910 G1911 K1912
• Binding residue (residue number reindexed from 1): V1821 G1850 T1851 G1852 K1853
• 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:7z8f, PDBe:7z8f, PDBj:7z8f
• PDBsum: 7z8f
• PubMed: 36071160
• UniProt: Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)