MolNFT v1 · #160241 · protein
GLUA2 in complex with its auxiliary subunit CNIH3 - MAP lbd-tmd-C3 - with antagonist ZK200775 -without ntd
6PEQ · Glutamate receptor 2: “GLUA2 in complex with its auxiliary subunit CNIH3 - MAP lbd-tmd-C3 - with antagonist ZK200775 -without ntd”. Electron microscopy, 3 ligands (PAM, ZK1, CLR), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6PEQ
- Type
- protein
- Length
- 2,044 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2; Protein cornichon homolog 3
- UniProt
- P19491, Q6ZWS4
- Ligands
- PAM, ZK1, CLR
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 2 | protein | 380 | 51% helix, 13% strand | P19491 |
| B, D | Glutamate receptor 2 | protein | 376 | 48% helix, 11% strand | P19491 |
| E, G | Protein cornichon homolog 3 | protein | 132 | 83% helix, 0% strand | Q6ZWS4 |
| F, H | Protein cornichon homolog 3 | protein | 134 | 83% helix, 0% strand | Q6ZWS4 |
Ligands and binding sites
- PAM · Palmitoleic acid · ligand · 14 copies · chains A, F, D, B, G, H, C, E
- ZK1 · {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid · ligand · 4 copies · chains A, B, C, D
- CLR · Cholesterol · ligand · 4 copies · chains A, E, B, F, G, C, H, D
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 8 copies · chains A, F, B, G, H, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.83 | 0.85 | 100 | ZK1 |
| 2 | 961 | 0.82 | 0.83 | 95 | empty |
| 3 | 223 | 0.69 | 0.85 | 35 | empty |
| 4 | 223 | 0.67 | 0.84 | 34 | empty |
| 5 | 298 | 0.66 | 0.81 | 28 | ZK1 |
Interfaces
13 interfaces between chains.
- B–C · 2701 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 2698 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1723 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1719 Ų buried · 8 hydrogen bonds · protein-protein
- H–C · 692 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PEQ · GluA2 in complex with its auxiliary subunit CNIH3 - map LBD-TMD-C3 - with antagonist… · the same entry in another collection · chain D against D, TM-score 1.00
- Q6ZWS4 · AlphaFold monomer V2.0 prediction for protein cornichon homolog 3 (Q6ZWS4) · a predicted model of the same protein · chain F against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P19491
- Every structure of UniProt Q6ZWS4
- Elsewhere: RCSB PDB 6PEQ · PDBe 6PEQ · UniProt P19491 · UniProt Q6ZWS4
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