Structure of PDB 8ss6 Chain A Binding Site BS04

Receptor Information

>8ss6 Chain A (length=974) Species: 10116 (Rattus norvegicus)

NSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVT
NAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPF
VIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQ
VTAINVGNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVI
TIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVDYDDSLVSKFI
ERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR
GNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTIN
IMELKTNGPRKIGYWSEVDKMVLTEDDTSGLEQKTVVVTTILESPYVMMK
KNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI
WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQK
SKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPNEFGIFNSLWF
SLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERM
VSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEP
SVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDS
KGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGECGATSAL
SLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAGRKALTLLSSVFAVCGL
GLLGIAVSTDYWLYLEEGIILPQNQSTEVKMSLHSGLWRVCFLAGEERGR
CFTIEYVMVNVLKMIRSATPFPLVSLFFMFIGFILSNIGHIRPHRTILAF
VSGIFFILSGLSLVVGLVLYISSINDEMLNRTKDAETYFNYKYGWSFAFA
AISFLLTESAGVMSVYLFMKRYTA

Ligand information

• Ligand ID: CLR
• InChI: InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
• InChIKey: HVYWMOMLDIMFJA-DPAQBDIFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
  CACTVS 3.341: CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
  ACDLabs 10.04: OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
  OpenEye OEToolkits 1.5.0: CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
  CACTVS 3.341: CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
• Formula: C27 H46 O
• Name: CHOLESTEROL
• ChEMBL: CHEMBL112570
• DrugBank: DB04540
• ZINC: ZINC000003875383
• PDB chain: 8ss6 Chain B Residue 1107

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ss6 Modulation of GluA2-gamma 5 synaptic complex desensitization, polyamine block and antiepileptic perampanel inhibition by auxiliary subunit cornichon-2.
• Resolution: 3.01 Å
• Binding residue (original residue number in PDB): F931 L979
• Binding residue (residue number reindexed from 1): F871 L919
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0000149 SNARE binding
• GO:0001540 amyloid-beta binding
• GO:0004970 glutamate-gated receptor activity
• GO:0004971 AMPA glutamate receptor activity
• GO:0005230 extracellular ligand-gated monoatomic ion channel activity
• GO:0005234 extracellularly glutamate-gated ion channel activity
• GO:0005515 protein binding
• GO:0008092 cytoskeletal protein binding
• GO:0015276 ligand-gated monoatomic ion channel activity
• GO:0015277 kainate selective glutamate receptor activity
• GO:0019865 immunoglobulin binding
• GO:0019901 protein kinase binding
• GO:0022849 glutamate-gated calcium ion channel activity
• GO:0030165 PDZ domain binding
• GO:0035254 glutamate receptor binding
• GO:0035255 ionotropic glutamate receptor binding
• GO:0038023 signaling receptor activity
• GO:0042802 identical protein binding
• GO:0044877 protein-containing complex binding
• GO:0097110 scaffold protein binding
• GO:0099094 ligand-gated monoatomic cation channel activity
• GO:0099507 ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential
• GO:1904315 transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential

Biological Process

• GO:0001919 regulation of receptor recycling
• GO:0006816 calcium ion transport
• GO:0007268 chemical synaptic transmission
• GO:0010226 response to lithium ion
• GO:0019722 calcium-mediated signaling
• GO:0021987 cerebral cortex development
• GO:0031623 receptor internalization
• GO:0034220 monoatomic ion transmembrane transport
• GO:0035235 ionotropic glutamate receptor signaling pathway
• GO:0035249 synaptic transmission, glutamatergic
• GO:0045184 establishment of protein localization
• GO:0050804 modulation of chemical synaptic transmission
• GO:0050806 positive regulation of synaptic transmission
• GO:0051262 protein tetramerization
• GO:0051966 regulation of synaptic transmission, glutamatergic
• GO:0060078 regulation of postsynaptic membrane potential
• GO:0060079 excitatory postsynaptic potential
• GO:0060992 response to fungicide
• GO:0098655 monoatomic cation transmembrane transport
• GO:0099505 regulation of presynaptic membrane potential
• GO:1905430 cellular response to glycine
• GO:1990416 cellular response to brain-derived neurotrophic factor stimulus

Cellular Component

• GO:0005783 endoplasmic reticulum
• GO:0005886 plasma membrane
• GO:0008021 synaptic vesicle
• GO:0008328 ionotropic glutamate receptor complex
• GO:0009986 cell surface
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0030424 axon
• GO:0030425 dendrite
• GO:0030426 growth cone
• GO:0030672 synaptic vesicle membrane
• GO:0032279 asymmetric synapse
• GO:0032281 AMPA glutamate receptor complex
• GO:0032590 dendrite membrane
• GO:0032839 dendrite cytoplasm
• GO:0032991 protein-containing complex
• GO:0036477 somatodendritic compartment
• GO:0042734 presynaptic membrane
• GO:0043005 neuron projection
• GO:0043025 neuronal cell body
• GO:0043195 terminal bouton
• GO:0043197 dendritic spine
• GO:0043198 dendritic shaft
• GO:0043204 perikaryon
• GO:0044326 dendritic spine neck
• GO:0044327 dendritic spine head
• GO:0045202 synapse
• GO:0045211 postsynaptic membrane
• GO:0048787 presynaptic active zone membrane
• GO:0097060 synaptic membrane
• GO:0098685 Schaffer collateral - CA1 synapse
• GO:0098793 presynapse
• GO:0098839 postsynaptic density membrane
• GO:0098978 glutamatergic synapse
• GO:0099544 perisynaptic space
• GO:0106033 spine synapse

External links

• PDB: RCSB:8ss6, PDBe:8ss6, PDBj:8ss6
• PDBsum: 8ss6
• PubMed: 37653241
• UniProt: P19491|GRIA2_RAT Glutamate receptor 2 (Gene Name=Gria2);
  Q8VHW8