Research workbench
Architecture and subunit arrangement of native AMPA receptors
Analyse Architecture and subunit arrangement of native AMPA receptors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NJN
- Type
- protein
- Length
- 5,212 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 1; Glutamate receptor 2; Glutamate receptor 3; A'-C' auxiliary…
- UniProt
- P19490, P19491, P19492, Q71RJ2
- Ligands
- ZK1, NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 1 | protein | 785 | 42% helix, 17% strand | P19490 |
| B, D | Glutamate receptor 2 | protein | 782 | 40% helix, 16% strand | P19491 |
| C | Glutamate receptor 3 | protein | 784 | 42% helix, 17% strand | P19492 |
| E, G | A'-C' auxiliary proteins | protein | 117 | 93% helix, 0% strand | — |
| F, H | Voltage-dependent calcium channel gamma-2 subunit | protein | 169 | 69% helix, 9% strand | Q71RJ2 |
| I | 11B8 scfv | protein | 224 | 1% helix, 50% strand | — |
| J, N | 15F1 Fab light chain | protein | 211 | 5% helix, 47% strand | — |
| K, O | 15F1 Fab heavy chain | protein | 215 | 0% helix, 52% strand | — |
| L | 5B2 Fab | protein | 218 | 3% helix, 54% strand | — |
| M | 5B2 Fab | protein | 213 | 5% helix, 50% strand | — |
Ligands and binding sites
- 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains B
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 | 805 | 0.85 | 0.88 | 127 | ZK1 |
| 2 | 926 | 0.84 | 0.86 | 102 | empty |
| 3 | 474 | 0.82 | 0.89 | 78 | empty |
| 4 | 1080 | 0.81 | 0.83 | 104 | empty |
| 5 | 614 | 0.81 | 0.86 | 79 | ZK1 |
Interfaces
24 interfaces between chains.
- A–B · 3593 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 3455 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2813 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2765 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 668 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 10 disulfide (N-glycosylation, disulfide, O-glycosylation, glycation, glycosylation).
Compared structures
- 6NJN · Architecture and subunit arrangement of native AMPA receptors · the same entry in another collection · chain K against K, TM-score 1.00
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 P19492
- Every structure of UniProt Q71RJ2
- Elsewhere: RCSB PDB 6NJN · PDBe 6NJN · UniProt P19490 · UniProt P19491 · UniProt P19492 · UniProt Q71RJ2
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