Structure of PDB 8fdu Chain A Binding Site BS02

Receptor Information
>8fdu Chain A (length=1001) Species: 9606,300852 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKVPQIEVETHKVAAPDVVVPTLDTVRHEALLYTWLAEHKPLVLCGPPGS
GKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHYCEYRRTPNGVV
LAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQT
WVKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYG
TFNRAMLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREM
TRWVRGIFEALRPLETLPVEGLIRIWAHEALRLFQDRLVEDEERRWTDEN
IDTVALKHFPNIDREKAMSRPILYSNWLSKDYIPVDQEELRDYVKARLKV
FYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVSGAGKTTLSRF
VAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNV
LDSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEE
LYKWFTSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWST
EALYQVGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPSHREAIVNSCVF
VHQTLHQANARLAKRGGRTMAITPRHYLDFINHYANLFHEKRSELEEQQM
HLNVGLRKIKETVDQVEELRRKVNRSTALLKSLSAERERWEKTSETFKNQ
MSTIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIAR
TEYLSNADERLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEF
IMNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVL
NREVRRTGGRVLITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFV
NFTVTRSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKSL
LQALNEVKGRILDDDTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQ
Q
Ligand information
Ligand IDADP
InChIInChI=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
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8fdu Chain A Residue 3202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8fdu Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		V1452 P1453 L1454 V1455 S1484 G1485 A1486 G1487 K1488 T1489 T1490 W1642 L1722
Binding residue
(residue number reindexed from 1)		V358 P359 L360 V361 S390 G391 A392 G393 K394 T395 T396 W548 L628
Annotation score5
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8fdu, PDBe:8fdu, PDBj:8fdu
PDBsum8fdu
PubMed37322240
UniProtQ14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1);
Q5SJX7

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