Structure of PDB 3vkg Chain B Binding Site BS02

Receptor Information
>3vkg Chain B (length=2853) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVNYQRKCKLVRGWDDLFNKLAEHLNSISHWDDRLNKVRSLLDVWIDVQR
RWVYLEGIFSGSGDINQLLPAESTRFKSINSEFIAILKKVSGAPLILEVL
AIERIQQTMERLSDLLGKVQKALGEYLERQRSAFARFYFVGDEDLLEIIG
NSKDIIKIQKHFRKMFAGLANLTLDDEKTTIIGMSSAEGETVTFKKPISI
ANGPKIHEWLTMVESEMKSTLATLLSESLQHFNQVDVNDHSKYSEWVDNY
PTQLVLLTSQIVWSTQVDQALGGGTLQQSKIQEQLQSIEQTTQMILNNLA
DSVLQDLSAQKRKKFEHLITELVHQRDVVRQLQKCKNLTGNKDFDWLYHM
RYYYDATQENVLHKLVIHMANATFYYGFEYLGIGERLVQTPLTDRCYLTL
TQALESRMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMS
RIFVGLCQCGAWGCFDEFNRLEERILSAVSQQIQTIQVALKENSKEVNIS
LHQDMGIFVTMNPGYAGRSNLPDNLKKLFRSMAMIKPDREMIAQVMLYSQ
GFKTAEVLAGKIVPLFKLCQEQLSAQSHYDFGLRALKSVLVSAGGIKRKC
ITDAESKTKADQIYCQYEIGVLLNSINDTMIPKLVADDIPLIQSLLLDVF
PGLQPIQMDQLRKKIQEIAKQRHLVTKQEWVEKILQLHQILNINHGVMMV
GPSGGGKTTSWEVYLEAIEQVDNIKSEAHVMDPKAITKDQLFGSLDLTTR
EWTDGLFTATLRRIIDNVRGESTKRHWIIFDGDVDPEWVENLNSLLDDNK
LLTLPNGERLALPNNVRVMFEVQDLKYATLATISRCGMVWFSEEILTTQM
IFQNYLDTLSNEPFDPQEAGLKVQKECAAIISQYFEPGGLVHKVLEDAGQ
RPHIMDFTRLRVLNSFFSLMNRSIVNVIEYNQLHSDFPMSPENQSNYITN
RLLYSLMWGLGGSMGLVERENFSKFIQTIAITPVPANTIPLLDYSVSIDD
ANWSLWKNKVEVETHKVASPDVVIPTVDTTRHVDVLHAWLSEHRPLILCG
PPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTP
SGETVLRPTQLGKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWR
TSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSSL
TQIYGTFNRALMKLLPNLRSFADNLTDAMVEFYSESQKRFTPDIQAHYIY
SPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLFQDRLVETEEKE
WTDKKIDEVALKHFPSVNLDALKRPILYSNWLTKDYQPVNRSDLREYVKA
RLKVFYEEELDVPLVLFNEVLDHILRIDRVFRQPQGHALLIGVSGGGKSV
LSRFVAWMNGLSIYTIKVNNNYKSSDFDDDLRMLLKRAGCKEEKICFIFD
ESNVLESSFLERMNTLLAGGEEGEEFTALMHACKETAQRSEEELYKYFTS
QVRRNLHVVFTMNPASPDFHNRSATSPALFNRCVLDWFGEWSPEALFQVG
SEFTRNLDLENPQYIAPPVFIQEAEIMMAIPPSHRDAVVSSLVYIHQTIG
EANIRLLKRQGRQNYVTPRHYLDFINQVVLLINEKRDQLEEEQLHLNIGL
KKLRDTEAQVKDLQVSLAQKNRELDVKNEQANQKLKQMVQDQQAAEIKQK
DARELQVQLDVRNKEIAVQEQLENAANELKLKQDEIVATITALEKSIATY
KEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFN
TQMSTVVGDVVLASAFLAYIGFFDQNFRTDLMRKWMIRLDSVGIKFKSDL
SVPSFLSKPEERLNWHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAM
EFLMNQYADKKITKTSFLDSSFMKNLESALRFGCPLLVQDVENIDPVLNP
VLNKPSFMIFLFTRDPTAHFTPDLCSRVTFVNFTVTPSSLQSQCLHEALK
TERPDTHKKRSDLLKIQGEFQVKLRILEKSLLNALSQASGNILDDDSVIS
TLETLKKETTEIALKVEETETVMQEISEVSALYNPMALSCSRVYFAMEEL
SQFHLYQFSLRAFLDIFYNLLNNNPNLVDKKDPNERLVYLSKDIFSMTFN
RVTRTLLNDDKLTFALQLTIISVKGTSNEIEESEWDFLLKGGDNLTSIKE
TIPQLDSLLSTTQQKWLICLRQQVPSFSKLVDHIQQNSSDWKQFFGKDQV
GEPIIPESWIVAQAQLSNQQSTIVSNFRKILLMKAFHSDRVLQYSHSFVC
SVFGEDFLNTQELDMANIVEKEVKSSSPLLLCSVPGYDASSKVDDLALQL
HKQYKSFAIGSPEGFELAEKSIYAAAKSGTWVLLKNIHLAPQWLVQLEKK
LHSLSPHPSFRLFMTSEIHPALPANLLRMSNVFSYENPPGVKANLLHTFI
GIPATRMDKQPAERSRIYFLLAWFHAIIQERLRYIPLGWTKFFEFNDADL
RGALDSIDYWVDLYSKGRSNIDPDKIPWIAVRTILGSTIYGGRIDNEFDM
RLLYSFLEQLFTPSAFNPDFPLVPSIGLSVPEGTTRAHFMKWIEALPEIS
TPIWLGLPENAESLLLSNKARKMINDLQKMQSSESSSEDKGKAKLKRIKD
PLFRCFEREISTGGKLVKKITNDLANLLELKSTNYLRSLTTSISKGIVPK
EWKWYSVPETISLSVWISDFSKRMQQLSEISESQVWLGGLLNPEAYITAT
RQSASQLNGWENLRLHASSFNVKGMALEGAVWNNDQLTPTDILSTPISIA
TLTWKDKDKLSVPVYLNETRSELLFSIDLPYDQSTSKQNWYQRSVSISSW
KSD
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 chain3vkg Chain B Residue 9008 [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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PDB3vkg The 2.8 A crystal structure of the dynein motor domain
Resolution2.81 Å
Binding residue
(original residue number in PDB)		V2250 W2255 G2279 G2281 K2282 T2283 T2284 E2396 L2421 M2425 N2429 R2809
Binding residue
(residue number reindexed from 1)		V675 W680 G704 G706 K707 T708 T709 E821 L846 M850 N854 R1185
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:3vkg, PDBe:3vkg, PDBj:3vkg
PDBsum3vkg
PubMed22398446
UniProtP34036|DYHC_DICDI Dynein heavy chain, cytoplasmic (Gene Name=dhcA)

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