Structure of PDB 6gkh Chain A Binding Site BS03

Receptor Information

>6gkh Chain A (length=685) Species: 10090 (Mus musculus)

ELQLRPYQMEVAQPALDGKNIIICLPTGSGKTRVAVYITKDHLDKKKQAS
ESGKVIVLVNKVMLAEQLFRKEFNPYLKKWYRIIGLSGDTQLKISFPEVV
KSYDVIISTAQILENSLLNLESGDDDGVQLSDFSLIIIDECHHTNKEAVY
NNIMRRYLKQKLRNNDLKKQNKPAIPLPQILGLTASPGVGAAKKQSEAEK
HILNICANLDAFTIKTVKENLGQLKHQIKEPCKKFVIADDTRENPFKEKL
LEIMASIQTYCQKSPMSDFGTQHYEQWAIQMEKKAAKDGNRKDRVCAEHL
RKYNEALQINDTIRMIDAYSHLETFYTDEKEKKFAVLNDKSLKLDETDEF
LMNLFFDNKKMLKKLAENPKYENEKLIKLRNTILEQFTRSEESSRGIIFT
KTRQSTYALSQWIMENAKFAEVGVKAHHLIGAGHSSEVKPMTQTEQKEVI
SKFRTGEINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARA
DESTYVLVTSSGSGVTEREIVNDFREKMMYKAINRVQNMKPEEYAHKILE
LQVQSILEKKMKVKRSIAKQYNDNPSLITLLCKNCSMLVCSGENIHVIEK
MHHVNMTPEFKGLYIVRENQTNGEIICKCGQAWGTMMVHKGLDLPCLKIR
NFVVNFKNNSPKKQYKKWVELPIRFPDLDYSEYCL

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 6gkh Chain A Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gkh Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis.
• Resolution: 4.06 Å
• Binding residue (original residue number in PDB): Q308 L309 R310 G333 G335 K336 R338 D797 R824
• Binding residue (residue number reindexed from 1): Q3 L4 R5 G28 G30 K31 R33 D472 R499
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0003725 double-stranded RNA binding
• GO:0003727 single-stranded RNA binding
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0019904 protein domain specific binding
• GO:0038187 pattern recognition receptor activity
• GO:0042802 identical protein binding
• GO:0043021 ribonucleoprotein complex binding
• GO:0046872 metal ion binding

Biological Process

• GO:0002376 immune system process
• GO:0009615 response to virus
• GO:0016925 protein sumoylation
• GO:0032727 positive regulation of interferon-alpha production
• GO:0032728 positive regulation of interferon-beta production
• GO:0032755 positive regulation of interleukin-6 production
• GO:0032760 positive regulation of tumor necrosis factor production
• GO:0039530 MDA-5 signaling pathway
• GO:0045071 negative regulation of viral genome replication
• GO:0045087 innate immune response
• GO:0051259 protein complex oligomerization
• GO:0051607 defense response to virus
• GO:0060337 type I interferon-mediated signaling pathway
• GO:0060760 positive regulation of response to cytokine stimulus
• GO:0071360 cellular response to exogenous dsRNA
• GO:0098586 cellular response to virus
• GO:0140374 antiviral innate immune response

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion

External links

• PDB: RCSB:6gkh, PDBe:6gkh, PDBj:6gkh
• PDBsum: 6gkh
• PubMed: 30449722
• UniProt: Q8R5F7|IFIH1_MOUSE Interferon-induced helicase C domain-containing protein 1 (Gene Name=Ifih1)