Structure of PDB 8ptk Chain m

Receptor sequence

>8ptkm (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

3D structure

• PDB: 8ptk Molecular mechanism of dynein-dynactin complex assembly by LIS1
• Chain: m
• Resolution: 10.0 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ADP	m	L1879 V1880 A1908 G1909 T1910 G1911 K1912	L1820 V1821 A1849 G1850 T1851 G1852 K1853
BS02	ATP	m	L2191 T2192 S2228 G2229 K2230 S2231 M2373 R2726	L2128 T2129 S2165 G2166 K2167 S2168 M2310 R2663
BS03	ANP	m	V2569 G2598 G2600 K2601 T2602 M2603	V2506 G2535 G2537 K2538 T2539 M2540
BS04	ANP	m	L2909 V2910 G2940 G2942 K2943	L2846 V2847 G2877 G2879 K2880

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