MolNFT v1 · #119468 · protein
Crystal structure of the AMPA receptor GLUA2/A4 N-terminal domain heterodimer
5FWX · Glutamate receptor 2: “Crystal structure of the AMPA receptor GLUA2/A4 N-terminal domain heterodimer”. X-ray diffraction, 2 ligands (NAG, SO4), 18 pockets (best druggability 0.81). MolNFT v1 #119468 on GenesisL1: 3D structure…
- PDB
- 5FWX
- Type
- protein
- Length
- 1,457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2; Glutamate receptor 4
- UniProt
- P19491, P19493
- Ligands
- NAG, SO4
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 351 | 35% helix, 24% strand | P19491 |
| B | Glutamate receptor 4 | protein | 375 | 37% helix, 24% strand | P19493 |
| C | Glutamate receptor 2 | protein | 356 | 34% helix, 23% strand | P19491 |
| D | Glutamate receptor 4 | protein | 375 | 37% helix, 23% strand | P19493 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, D, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.81 | 0.85 | 76 | empty |
| 2 | 829 | 0.81 | 0.84 | 75 | empty |
| 3 | 473 | 0.78 | 0.86 | 70 | empty |
| 4 | 481 | 0.78 | 0.85 | 50 | SO4 |
| 5 | 146 | 0.68 | 0.88 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1347 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1323 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 963 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 894 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 301 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5FWX · Crystal structure of the AMPA receptor GluA2/A4 N-terminal domain heterodimer · the same entry in another collection · chain A against A, TM-score 1.00
- P19493 · AlphaFold monomer V2.0 prediction for glutamate receptor 4 (P19493) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P19493
- Elsewhere: RCSB PDB 5FWX · PDBe 5FWX · UniProt P19491 · UniProt P19493
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