Structure of PDB 8dzz Chain D Binding Site BS01

Receptor Information
>8dzz Chain D (length=2363) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFYWLDLYGILGENLDIQNFLPLETSKFKSLSLKMIKSSLSTFLERQRRQ
FPRFYFLGNDDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFFEDSITGVR
SVEGEVLNLNEKIELKDSIQAQEWLNILDTEIKLSVFTQFRDCLGQLKDG
TDIEVVVSKYIFQAILLSAQVMWTELVEKCLQTNEFSKYWKEVDMKIKGL
LDKLNKSSDNVKKKIEALLVEYLHFNNVIGQLKNCSTKEEARLLWAKVQK
FYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPLLLVGFATLT
DSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSR
LLVGITQIGAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLE
EETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSPQSGTIAEMI
LQIMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSPL
VSEFGEGEKTVVESLKRVILPSLGDTDELVFKDELSKIFDSNSKAIVQCL
KDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVI
DAMAIFDGHANVVYVIDTKVLTKESLYGSMLKATLEWRDGLFTSILRRVN
DDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPP
NFRILFETDNLDHTTPATITRCGLLWFSTDVCSISSKIDHLLNKSYEALF
ELDKLKDLISDSFDMASLTNIFTCSNDLVHILGVRTFNKLETAVQLAVHL
ISSYRQWFQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINT
YFGHDSQELSDYSTIVILSFSSFCSEIPSVSLEAHEVMRPDIVIPTIDTI
KHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKD
TTTEHILSALHRHTNYVTGLTLLPKSDIKNLVLFCDQINLPKLDKYGSQN
VVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFT
RHAAILYLGYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARASVHLYN
ECKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYE
AWRIFADRLVGVKEKNSFEQLLYETVDKYLPLGNISSTSLLFSGLLSLDF
KEVNKTDLVNFIEERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQG
HMMLIGASRTGKTILTRFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAIS
DCSLKESRTCLIIDESNILETAFLERMNTLLANADIPDLFQGEEYDKLLN
NLRNKTRSLGLLLDTEQELYDWFVGEIAKNLHVVFTICDPTNNKSSAMIS
SPALFNRCIINWMGDWDTKTMSQVANNMVDVVPMEFTDFIVPEVNKELVF
TEPIQTIRDAVVNILIHFDRNFYQKMKVGVNPRSPGYFIDGLRALVKLVT
AKYQDLQENQRFVNVGLEKLNESVLKVNELNKTLSKKSTELTEKEKEARS
TLDKSKQKYSLLIRDVEAIKTEMSNVQANLDRSISLVKSLTFEKERWLNT
TKQFSKTSQELIGNCIISSIYETYFGHLNERERGDMLVILKRLLGKFAVK
YDVNYRFIDYLVTLDEKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLD
PSSHMITVISNYYGNKTVLLSFLEEGFVKRLENAVRFGSVVIIQDGEFFD
PIISRLISREFNHAGNRVTVEIGDHEVDVSGDFKLFIHSCDPSGDIPIFL
RSRVRLVHFVTNKESIETRIFDITLTEENAEMQRKREDLIKLNTEYRLKL
KNLEKRLLEELNNSQGNMLENDELMVTLNNLKKEAMNIEKKLSESEEFFP
QFDNLVEEYSIIGKHSVKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFIK
TRVDEILWLLYQEVYCQFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEA
VLTMIGVLSESSDGVPKLTNDDLRYLWDYVTTKSYISALNWFKNEFFVDE
WNIADVVANSENNYFTMASERDVDGTFKLIELAKASKESLKIIPLGSIEN
LNYAQEEISKSKIEGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKF
KMFMTCHLTGDKLPAPLLQRTDRVVYEDIPGILDTVKDLWGSQGVWSVYC
TFLLSWFHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTN
NIPWAQVRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVR
IPQPLLQQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILDYERLQA
KEVASSTEQLLQE
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8dzz Chain D Residue 4201 [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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PDB8dzz Lis1 relieves cytoplasmic dynein-1 autoinhibition by acting as a molecular wedge.
Resolution4.1 Å
Binding residue
(original residue number in PDB)		F2047 S2048 G2077 C2078 G2079 K2080 T2081 A2082 E2195 C2220 K2225 H2228 R2549
Binding residue
(residue number reindexed from 1)		F559 S560 G589 C590 G591 K592 T593 A594 E707 C732 K737 H740 R1048
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
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:8dzz, PDBe:8dzz, PDBj:8dzz
PDBsum8dzz
PubMed37620585
UniProtP36022|DYHC_YEAST Dynein heavy chain, cytoplasmic (Gene Name=DYN1)

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