MolNFT v1 · #125179 · protein
AMPA subtype ionotropic glutamate receptor GLUA2 in apo state
5L1B · Glutamate receptor 2,GLUTAMATE receptor 2: “AMPA subtype ionotropic glutamate receptor GLUA2 in apo state”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #125179 on GenesisL1: 3D structure…
- PDB
- 5L1B
- Type
- protein
- Length
- 3,123 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2,GLUTAMATE receptor 2
- UniProt
- P19491
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 780 | 40% helix, 17% strand | P19491 |
| D | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 783 | 39% helix, 19% strand | P19491 |
Ligands and binding sites
- 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 | 1103 | 0.85 | 0.86 | 113 | empty |
| 2 | 1141 | 0.83 | 0.84 | 98 | empty |
| 3 | 802 | 0.83 | 0.86 | 66 | empty |
| 4 | 973 | 0.76 | 0.79 | 94 | empty |
| 5 | 670 | 0.72 | 0.79 | 82 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3599 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 3283 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 3179 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 3061 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 405 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5L1B · AMPA subtype ionotropic glutamate receptor GluA2 in 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 5L1B · PDBe 5L1B · UniProt P19491
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