MolNFT v1 · #61558 · protein
Crystal structure of the binding domain of the AMPA subunit GLUR2 bound to glutamate
3DP6 · Glutamate receptor 2: “Crystal structure of the binding domain of the AMPA subunit GLUR2 bound to glutamate”. X-ray diffraction, 2 ligands (GLU, ZN), 8 pockets (best druggability 0.79). MolNFT v1 #61558 on GenesisL1: 3D structure…
- PDB
- 3DP6
- Type
- protein
- Length
- 774 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, ZN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor 2 | protein | 258 | 39% helix, 21% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.79 | 0.86 | 85 | empty |
| 2 | 507 | 0.70 | 0.80 | 51 | empty |
| 3 | 271 | 0.58 | 0.78 | 32 | empty |
| 4 | 99 | 0.38 | 0.75 | 22 | empty |
| 5 | 72 | 0.37 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1007 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 284 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3DP6 · Crystal structure of the binding domain of the AMPA subunit GluR2 bound to glutamate · the same entry in another collection · chain B against B, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain A 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
- Elsewhere: RCSB PDB 3DP6 · PDBe 3DP6 · UniProt P19491
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