Structure of PDB 8fcy Chain A Binding Site BS04

Receptor Information

>8fcy Chain A (length=2864) Species: 9606,300852

LKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVKEHINSVSAMKLSPY
YKVFEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSADIKHLLP
VETQRFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGKIQ
KALGEYLERERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVS
SIILNEDNSVVLGISSREGEEVMFKTPVSITEHPKINEWLTLVEKEMRVT
LAKLLAESVTEVEIFGKATSIDPNTYITWIDKYQAQLVVLSAQIAWSENV
ETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQPPLRRRKLEHLI
TELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSIQMA
NAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAGTGK
TESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNR
LEERMLSAVSQQVQCIQEALREHSNPNYDKTSAPITCELLNKQVKVSPDM
AIFITMNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQGFRTAEVLANKIV
PFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRERIQKIKREIAENLP
EQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGVQYHRGEMTALREEL
KKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGLMMVGPSGSGKSM
AWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDPNTREWTDGLFTH
VLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLDDNKLLTLPNGER
LSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDVLSTDMIFNNFLARL
RSIPLSPMLQIQRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRC
LGSLFSMLHQACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLSG
DSRLKMRAELGEYIRRITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQ
IEVETHKVAAPDVVVPTLDTVRHEALLYTWLAEHKPLVLCGPPGSGKTMT
LFSALRALPDMEVVGLNFSSATTPELLLKTFDHYCEYRRTPNGVVLAPVQ
LGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQTWVKLE
RIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRA
MLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWVR
GIFEALRPLETLPVEGLIRIWAHEALRLFQDRLVEDEERRWTDENIDTVA
LKHFPNIDREKAMSRPILYSNWLSKDYIPVDQEELRDYVKARLKVFYEEE
LDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVSGAGKTTLSRFVAWMN
GLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNVLDSGF
LERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWF
TSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALYQ
VGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTL
HQANARLAKRGGRTMAITPRHYLDFINHYANLFHEKRSELEEQQMHLNVG
LRKIKETVDQVEELRRKVNRSTALLKSLSAERERWEKTSETFKNQMSTIA
GDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLS
NADERLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEY
KDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVR
RTGGRVLITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVT
RSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALN
EVKGRILDDDTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQQYLPL
STACSSIYFTMESLKQIHFLYQYSLQFFLDIYHNVLYENPNLKGVTDHTQ
RLSIITKDLFQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPTYDAE
FQHFLRGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQAD
EQFGIWLDSSSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLAM
AHMFVSTNLGESFMSIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGH
VEDLAAEQNTQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLAPG
WLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVK
ANMLRTFSSIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKK
YEFGESDLRSACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGG
RVDNEFDQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREE
FVQWVELLPDTQTPSWLGLPNNAERVLLTTQGVDMISKMLKMQAWMRTLH
TTASNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKLLQDVRQDL
ADVVQVCEGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSD
FSERIKQLQNISLAAASGGAKELKNIHVCLGGLFVPEAYITATRQYVAQA
NSWSLEELCLEVNVTTSQGATLDACSFGVTGLKLQGATCNNNKLSLSNAI
STALPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIFTVDFEIATKED
PRSFYERGVAVLCT

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: 8fcy Chain A Residue 3204

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fcy Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): L1454 V1455 S1484 G1485 G1487 K1488 T1489 T1490
• Binding residue (residue number reindexed from 1): L1405 V1406 S1435 G1436 G1438 K1439 T1440 T1441
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 6.1.1.11: serine--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide 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

Cellular Component

• GO:0030286 dynein complex

External links

• PDB: RCSB:8fcy, PDBe:8fcy, PDBj:8fcy
• PDBsum: 8fcy
• PubMed: 37322240
• UniProt: Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1);
  Q5SJX7