MolNFT v1 · #107193 · protein
Full-length AMPA subtype ionotropic glutamate receptor GLUA2 in the apo state
4U2P · Glutamate receptor 2: “Full-length AMPA subtype ionotropic glutamate receptor GLUA2 in the apo state”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #107193 on GenesisL1: 3D structure, binding…
- PDB
- 4U2P
- Type
- protein
- Length
- 3,022 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 755 | 40% helix, 19% strand | P19491 |
| B | Glutamate receptor 2 | protein | 761 | 40% helix, 19% strand | P19491 |
| D | Glutamate receptor 2 | protein | 751 | 41% helix, 20% strand | P19491 |
| C | Glutamate receptor 2 | protein | 755 | 41% helix, 19% strand | P19491 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, D, C
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 | 948 | 0.82 | 0.83 | 77 | empty |
| 2 | 1014 | 0.81 | 0.82 | 85 | empty |
| 3 | 797 | 0.81 | 0.84 | 90 | empty |
| 4 | 986 | 0.80 | 0.81 | 92 | empty |
| 5 | 547 | 0.76 | 0.83 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3132 Ų buried · 19 hydrogen bonds · protein-protein
- D–C · 2643 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2278 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 2235 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 422 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4U2P · Full-length AMPA subtype ionotropic glutamate receptor GluA2 in the apo state · 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 4U2P · PDBe 4U2P · UniProt P19491
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