Structure of PDB 5nug Chain A Binding Site BS03

Receptor Information
>5nug Chain A (length=2920) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIVKDVLLVAQGEMALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDL
FNKVKEHINSVSAMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRR
WVYLEGIFTGSADIKHLLPVETQRFQSISTEFLALMKKVSKSPLVMDVLN
IQGVQRSLERLADLLGKIQKALGEYLERERSSFPRFYFVGDEDLLEIIGN
SKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSREGEEVMFKTPVSIT
EHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYITWID
KYQAQLVVLSAQIAWSENVETALSSAAPLHSVLSNVEVTLNVLADSVLME
QPPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPK
QTDVLQQLSIQMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEAR
LGGSPFGPAGTGKTESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLC
QVGAWGCFDEFNRLEERMLSAVSQQVQCIQEALREHSNPITCELLNKQVK
VSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQ
GFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRER
IQKIKREAENLPEQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGVQY
HRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGL
MMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDP
NTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLD
DNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDVLS
TDMIFNNFLARLRSIPLDEASPMLQIQRDAATIMQPYFTSNGLVTKALEH
AFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQYNANHPDFPMQIEQLERY
IQRYLVYAILWSLSGDSRLKMRAELGEYIRRITTVPLPTAPNIPIIDYEV
SISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEALLYTWLAEHK
PLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHYC
EYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEH
GGFYRTSDQTWVKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYP
GPASLTQIYGTFNRAMLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQDTQ
PHYIYSPREMTRWVRGIFEALRPLETLPVEGLIRIWAHEALRLFQDRLVE
DEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLSKDYIPVDQEEL
RDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVS
GAGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEK
IAFIMDESNVLDSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQK
EGLMLDSHEELYKWFTSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNRC
VLNWFGDWSTEALYQVGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPSH
REAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFINHYANLFHE
KRSELEEQQMHLNVGLRKIKETVDQVEELRRDLRIKSQELEVKNAAANDK
LKKMVKDQQEAEKKQMIRDLEASIARYKEEYAVLISEAQAIKADLAAVEA
KVNRSTALLKSLSAERERWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYF
DQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADERLRWQASSLPAD
DLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEYKDRKITRTSFLDDAFR
KNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRVLITLGDQDID
LSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAE
RPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDDDTIITTL
ENLKREAAEVTRKVEETDIVMQEVETVSQQYLPLSTACSSIYFTMESLKQ
IHFLYQYSLQFFLDIYHNVLYENPNLVTDHTQRLSIITKDLFQVAFNRVA
RGMLHQDHITFAMLLARIKLKGTGEPTYDAEFQHFLRGNEIVLSAGSTPR
IQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDSSSPEQTVPYL
WTPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSIMEQPLD
LTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEG
FNQADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHACFRLFL
TMEINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFSSIPVSRICKSPNER
ARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLRSACDTVDTWLDDT
AKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQRLLNTFLERLFTTR
SFDSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSWLGLPNN
AERVLLTTQGVDMISKMLKMQMLETLHTTASNWLHLIPQTLSHLKRTENI
KDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEGKKKQTNYLRTLINEL
VKGILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAASKELKNIH
VCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVSFGVTGLKLQGAT
CNNNKLSLSNAISTALPLTQLRWVKQSVVTLPVYLNFTRADLIFTVDFEI
ATKEDPRSFYERGVAVLCTE
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5nug Chain A Residue 4803 [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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PDB5nug Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		S2231 E2344
Binding residue
(residue number reindexed from 1)		S761 E874
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein 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
GO:0007052 mitotic spindle organization
GO:0007097 nuclear migration
GO:0008090 retrograde axonal transport
GO:0031122 cytoplasmic microtubule organization
GO:0032388 positive regulation of intracellular transport
GO:0033962 P-body assembly
GO:0034063 stress granule assembly
GO:0051293 establishment of spindle localization
GO:0051301 cell division
GO:0060236 regulation of mitotic spindle organization
GO:0090235 regulation of metaphase plate congression
GO:0120162 positive regulation of cold-induced thermogenesis
GO:1905832 positive regulation of spindle assembly
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005868 cytoplasmic dynein complex
GO:0005874 microtubule
GO:0005881 cytoplasmic microtubule
GO:0005938 cell cortex
GO:0016020 membrane
GO:0030175 filopodium
GO:0030286 dynein complex
GO:0035578 azurophil granule lumen
GO:0070062 extracellular exosome
GO:1904115 axon cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5nug, PDBe:5nug, PDBj:5nug
PDBsum5nug
PubMed28602352
UniProtQ14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)

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