MolNFT v1 · #125182 · protein
AMPA subtype ionotropic glutamate receptor GLUA2 in complex with noncompetitive inhibitor perampanel
5L1F · Glutamate receptor 2: “AMPA subtype ionotropic glutamate receptor GLUA2 in complex with noncompetitive inhibitor perampanel”. X-ray diffraction, 2 ligands (6ZP, NAG), 20 pockets (best druggability 0.82). MolNFT v1 #125182 on…
- PDB
- 5L1F
- Type
- protein
- Length
- 3,100 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- 6ZP, NAG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glutamate receptor 2 | protein | 777 | 40% helix, 18% strand | P19491 |
| B, C | Glutamate receptor 2 | protein | 773 | 38% helix, 17% strand | P19491 |
Ligands and binding sites
- 6ZP · 2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, 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 | 889 | 0.82 | 0.84 | 111 | empty |
| 2 | 1186 | 0.81 | 0.82 | 90 | empty |
| 3 | 945 | 0.81 | 0.82 | 109 | 6ZP |
| 4 | 632 | 0.78 | 0.84 | 72 | empty |
| 5 | 824 | 0.76 | 0.80 | 82 | 6ZP |
Interfaces
6 interfaces between chains.
- A–B · 3842 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 3501 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 3025 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 3007 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 394 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 6 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 5L1F · AMPA subtype ionotropic glutamate receptor GluA2 in complex with noncompetitive inhibitor… · the same entry in another collection · chain A against A, 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 P19491
- Elsewhere: RCSB PDB 5L1F · PDBe 5L1F · UniProt P19491
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