MolNFT v1 · #161629 · protein
GLUA1/2 in complex with auxiliary subunit gamma-8
6QKC · Glutamate receptor 1: “GLUA1/2 in complex with auxiliary subunit gamma-8”. Electron microscopy, 1 ligand (E2Q), 20 pockets (best druggability 0.85). MolNFT v1 #161629 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QKC
- Type
- protein
- Length
- 1,902 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 1; Glutamate receptor 2; Voltage-dependent calcium channel gamma-8…
- UniProt
- P19490, P19491, Q8VHW5
- Ligands
- E2Q
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 1 | protein | 393 | 48% helix, 13% strand | P19490 |
| B, D | Glutamate receptor 2 | protein | 396 | 46% helix, 12% strand | P19491 |
| I, J | Voltage-dependent calcium channel gamma-8 subunit | protein | 162 | 65% helix, 9% strand | Q8VHW5 |
Ligands and binding sites
- E2Q · 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide · ligand · 4 copies · chains A, B, C, D
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 12 copies · chains A, J, B, C, I, 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 | 1167 | 0.85 | 0.85 | 138 | E2Q |
| 2 | 1030 | 0.85 | 0.86 | 117 | E2Q |
| 3 | 191 | 0.80 | 0.94 | 22 | empty |
| 4 | 108 | 0.75 | 0.95 | 38 | empty |
| 5 | 220 | 0.72 | 0.88 | 41 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2957 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2948 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2113 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 2099 Ų buried · 7 hydrogen bonds · protein-protein
- C–I · 761 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6QKC · GluA1/2 In complex with auxiliary subunit gamma-8 · the same entry in another collection · chain J against J, 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 J against A, TM-score 0.95
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain B against A, TM-score 0.90
- P19490 · AlphaFold monomer V2.0 prediction for glutamate receptor 1 (P19490) · a predicted model of the same protein · chain C against A, TM-score 0.64
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 Q8VHW5
- Elsewhere: RCSB PDB 6QKC · PDBe 6QKC · UniProt P19490 · UniProt P19491 · UniProt Q8VHW5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.