Structure of PDB 8dzz Chain D Binding Site BS03

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 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 chain8dzz Chain D Residue 4203 [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)		M2732 V2733 H2735 R2763 T2764 G2765 K2766 T2767 I2768 W2920 I2993 R3512
Binding residue
(residue number reindexed from 1)		M1228 V1229 H1231 R1259 T1260 G1261 K1262 T1263 I1264 W1416 I1489 R1803
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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