Structure of PDB 7z8g Chain A Binding Site BS01

Receptor Information

>7z8g Chain A (length=3047) Species: 9606 (Homo sapiens)

QDLKGVWSELSKVWEQIDQMKEQPWVSVQPRKLRQNLDALLNQLKSFPAR
LRQYASYEFVQRLLKGYMKINMLVIELKSEALKDRHWKQLMKRLHVNWVV
SELTLGQIWDVDLQKNEAIVKDVLLVAQGEMALEEFLKQIREVWNTYELD
LVNYQNKCRLIRGWDDLFNKVKEHINSVSAMKLSPYYKVFEEDALSWEDK
LNRIMALFDVWIDVQRRWVYLEGIFTGSADIKHLLPVETQEFQSISTEFL
ALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGEIQKALGEYLERERSSF
PRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGI
SSREGEEVMFKTPVSITEHPKINEWLTLVEKEMRVTLAKLLAESVTEVEI
FGKATSIDPNTYITWIDKYQAQLVVLSAQIAWSENVETALSSMGGGGDAA
PLHSVLSNVEVTLNVLADSVLMEQPPLRRRKLEHLITELVHQRDVTRSLI
KSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSIQMANAKFNYGFEYLGVQ
DKLVQTPLTDRCYLTMTQALEARLGGSPFGPAGTGKTESVKALGHQLGRF
VLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQ
CIQEALREHSNPNYDKTSAPITCELLNKQVKVSPDMAIFITMNPGSNLPD
NLKKLFRSLAMTKPDRQLIAQVMLYSQGFRTAEVLANKIVPFFKLCDEQL
SSQSHYDFGLRALKSVLVSAGNVKRERIQKIKREKEERGEAVDEGEIAEN
LPEQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGVQYHRGEMTALRE
ELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGLMMVGPSGSGK
SMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDPNTREWTDGLF
THVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLDDNKLLTLPNG
ERLSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDVLSTDMIFNNFLA
RLRSIPLDEGEDEAQRRRKGKEDEGEEAASPMLQIQRDAATIMQPYFTSN
GLVTKALEHAFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQYNANHPDFP
MQIEQLERYIQRYLVYAILWSLSGDSRLKMRAELGEYIRRITTVPLPTAP
NIPIIDYEVSISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEAL
LYTWLAEHKPLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPEL
LLKTFDHYCEYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVI
SFIRQMVEHGGFYRTSDQTWVKLERIQFVGACNPPTDPGRKPLSHRFLRH
VPVVYVDYPGPASLTQIYGTFNRAMLRLIPSLRTYAEPLTAAMVEFYTMS
QERFTQDTQPHYIYSPREMTRWVRGIFEALRPLETLPVEGLIRIWAHEAL
RLFQDRLVEDEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLSKD
YIPVDQEELRDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQ
GHLLLIGVSGAGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVL
RRSGCKNEKIAFIMDESNVLDSGFLERMNTLLANGEVPGLFEGDEYATLM
TQCKEGAQKEGLMLDSHEELYKWFTSQVIRNLHVVFTMNPSSEGLKDRAA
TSPALFNRCVLNWFGDWSTEALYQVGKEFTSKMDLEKPNYIVPDYMPVVY
DKLPQPPSHREAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFI
NHYANLFHEKRSELEEQQMHLNVGLRKIKETVDQVEELRRDAKVNRSTAL
LKSLSAERERWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYFDQQMRQNL
FTTWSHHLQQANIQFRTDIARTEYLSNADERLRWQASSLPADDLCTENAI
MLKRFNRYPLIIDPSGQATEFIMNEYKDRKITRTSFLDDAFRKNLESALR
FGNPLLVQDVESYDPVLNPVLNREVRRTGGRVLITLGDQDIDLSPSFVIF
LSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAERPDVDEKR
SDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDDDTIITTLENLKREAA
EVTRKVEETDIVMQEVETVSQQYLPLSTACSSIYFTMESLKQIHFLYQYS
LQFFLDIYHNVLYENPNLKGVTDHTQRLSIITKDLFQVAFNRVARGMLHQ
DHITFAMLLARIKLKGTVGEPTYDAEFQHFLRGNEIVLSAGSTPRIQGLT
VEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDSSSPEQTVPYLWSEET
PATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSIMEQPLDLT
HIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEGFN
QADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHACFRLFLTM
EINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFSSIPVSRICKSPNERAR
LYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLRSACDTVDTWLDDTAK
GRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQRLLNTFLERLFTTRSF
DSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSWLGLPNNAE
RVLLTTQGVDMISKMLKMQMLEDEDAWMRTLHTTASNWLHLIPQTLSHLK
RTVENIKDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEGKKKQTNYLR
TLINELVKGILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAASG
GAKELKNIHVCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVTTSQ
GATLDACSFGVTGLKLQGATCNNNKLSLSNAISTALPLTQLRWVKQTNTE
KKASVVTLPVYLNFTRADLIFTVDFEIATKEDPRSFYERGVAVLCTE

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: 7z8g Chain A Residue 4701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7z8g Structure of dynein-dynactin on microtubules shows tandem adaptor binding.
• Resolution: 3.52 Å
• Binding residue (original residue number in PDB): L1879 V1880 G1909 T1910 G1911 K1912 T1913 E1914 I2049 L2090 R2091 K2094
• Binding residue (residue number reindexed from 1): L553 V554 G583 T584 G585 K586 T587 E588 I719 L760 R761 K764
• 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:7z8g, PDBe:7z8g, PDBj:7z8g
• PDBsum: 7z8g
• PubMed: 36071160
• UniProt: Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)