Structure of PDB 6mdn Chain D Binding Site BS03

Receptor Information
>6mdn Chain D (length=713) Species: 10029 (Cricetulus griseus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLR
THPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEID
FLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVK
DIEAMRQKIEVGLVVGNSQVAFEKAENSSLNLIGKAKTIINPDWNFEKMG
IGGLDKEFSDIFRRAFASRVFPPEIVEQMGCKHVKGILLYGPPGCGKTLL
ARQIGKMLNAREPKVVNGPEILNKYVGESEANIRKLFADAEEEQRRLGAN
SGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKIDGVEQLNNILV
IGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRGHQL
LSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRHIIVDMEKAESLQV
TRGDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLV
QQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIG
FSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQA
LLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQ
LLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYR
VRKFLALLREEGA
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 chain6mdn Chain E Residue 802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6mdn Structural principles of SNARE complex recognition by the AAA+ protein NSF.
Resolution4.4 Å
Binding residue
(original residue number in PDB)		R385 R388
Binding residue
(residue number reindexed from 1)		R366 R369
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.6: vesicle-fusing ATPase.
Gene Ontology
Molecular Function
GO:0000149 SNARE binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0017075 syntaxin-1 binding
GO:0019901 protein kinase binding
GO:0019905 syntaxin binding
GO:0030165 PDZ domain binding
GO:0035255 ionotropic glutamate receptor binding
GO:0042802 identical protein binding
GO:0044877 protein-containing complex binding
GO:0046872 metal ion binding
GO:0140545 ATP-dependent protein disaggregase activity
Biological Process
GO:0001921 positive regulation of receptor recycling
GO:0006813 potassium ion transport
GO:0006886 intracellular protein transport
GO:0006891 intra-Golgi vesicle-mediated transport
GO:0015031 protein transport
GO:0035494 SNARE complex disassembly
GO:0043001 Golgi to plasma membrane protein transport
GO:0045732 positive regulation of protein catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0030496 midbody

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6mdn, PDBe:6mdn, PDBj:6mdn
PDBsum6mdn
PubMed30198481
UniProtP18708|NSF_CRIGR Vesicle-fusing ATPase (Gene Name=NSF)

[Back to BioLiP]