MolNFT v1 · #184069 · protein
Resting state GLUA1/A2 AMPA receptor in complex with tarp gamma 8 and CNIH2 (lbd-tmd)
7OCE · Glutamate receptor 1: “Resting state GLUA1/A2 AMPA receptor in complex with tarp gamma 8 and CNIH2 (lbd-tmd)”. Electron microscopy, 3 ligands (PC1, E2Q, CLR), 20 pockets (best druggability 0.83). MolNFT v1 #184069 on GenesisL1: 3D…
- PDB
- 7OCE
- Type
- protein
- Length
- 2,322 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 1; Glutamate receptor 2; Protein cornichon homolog 2…
- UniProt
- P19490, P19491, Q5BJU5, Q8VHW5
- Ligands
- PC1, E2Q, CLR
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 1 | protein | 410 | 47% helix, 14% strand | P19490 |
| B, D | Glutamate receptor 2 | protein | 408 | 47% helix, 12% strand | P19491 |
| G, E | Protein cornichon homolog 2 | protein | 158 | 80% helix, 0% strand | Q5BJU5 |
| I, J | Voltage-dependent calcium channel gamma-8 subunit | protein | 185 | 64% helix, 10% strand | Q8VHW5 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 46 copies · chains A, B, G, D, C, I, J, E
- E2Q · 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide · ligand · 4 copies · chains A, B, D, C
- CLR · Cholesterol · ligand · 2 copies · chains G, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.83 | 0.84 | 108 | E2Q |
| 2 | 210 | 0.82 | 0.96 | 28 | empty |
| 3 | 952 | 0.82 | 0.83 | 95 | empty |
| 4 | 177 | 0.70 | 0.88 | 38 | empty |
| 5 | 739 | 0.69 | 0.76 | 81 | empty |
Interfaces
13 interfaces between chains.
- D–C · 3400 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 3393 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2055 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 2047 Ų buried · 10 hydrogen bonds · protein-protein
- I–C · 780 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7OCE · Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD) · the same entry in another collection · chain E against E, TM-score 1.00
- Q8VHW5 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-8 subunit… · a predicted model of the same protein · chain I against A, TM-score 0.96
- Q5BJU5 · AlphaFold monomer V2.0 prediction for protein cornichon homolog 2 (Q5BJU5) · a predicted model of the same protein · chain G against A, TM-score 0.93
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 P19490
- Every structure of UniProt P19491
- Every structure of UniProt Q5BJU5
- Every structure of UniProt Q8VHW5
- Elsewhere: RCSB PDB 7OCE · PDBe 7OCE · UniProt P19490 · UniProt P19491 · UniProt Q5BJU5 · UniProt Q8VHW5
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