MolNFT v1 · #161649 · protein
Full length GLUA1/2-GAMMA8 complex
6QKZ: “Full length GLUA1/2-GAMMA8 complex”. Electron microscopy, 3 ligands (E2Q, NAG, BMA), 20 pockets (best druggability 0.72). MolNFT v1 #161649 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QKZ
- Type
- protein
- Length
- 3,386 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLUA1; Glutamate receptor 2; Voltage-dependent calcium channel gamma-8 subunit
- UniProt
- P19490, P19491, Q8VHW5
- Ligands
- E2Q, NAG, BMA
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | GLUA1 | protein | 759 | 44% helix, 18% strand | P19490 |
| B, D | Glutamate receptor 2 | protein | 772 | 40% helix, 18% 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.72 | 0.76 | 150 | empty |
| 2 | 1007 | 0.72 | 0.76 | 153 | empty |
| 3 | 883 | 0.71 | 0.77 | 128 | empty |
| 4 | 897 | 0.70 | 0.76 | 132 | empty |
| 5 | 617 | 0.68 | 0.78 | 73 | empty |
Interfaces
7 interfaces between chains.
- C–D · 355 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 345 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 323 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 312 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan (N-glycosylation).
Compared structures
- 6QKZ · Full length GluA1/2-gamma8 complex · 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
- P19490 · AlphaFold monomer V2.0 prediction for glutamate receptor 1 (P19490) · a predicted model of the same protein · chain C against A, TM-score 0.62
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain B against A, TM-score 0.50
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 6QKZ · PDBe 6QKZ · UniProt P19490 · UniProt P19491 · UniProt Q8VHW5
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