Research workbench
Crystal structure of the GLUA2 ligand-binding domain in complex with L-aspartate at 1.80 a resolution
Analyse Crystal structure of the GLUA2 ligand-binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O3A
- Type
- protein
- Length
- 786 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- ASP, ZN, CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 261 | 36% helix, 21% strand | P19491 |
| B | Glutamate receptor 2 | protein | 263 | 38% helix, 21% strand | P19491 |
| C | Glutamate receptor 2 | protein | 262 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 9 copies · chains A, C, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 12 copies · chains A, B, C
- ACT · Acetate ion · additive · 10 copies · chains A, C, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.72 | 0.76 | 79 | ACT, GOL, ZN |
| 2 | 787 | 0.69 | 0.76 | 94 | ACT, GOL |
| 3 | 479 | 0.65 | 0.77 | 43 | empty |
| 4 | 115 | 0.42 | 0.77 | 19 | empty |
| 5 | 74 | 0.32 | 0.74 | 14 | ACT |
Interfaces
3 interfaces between chains.
- B–C · 323 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 303 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 303 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4O3A · Crystal structure of the glua2 ligand-binding domain in complex with L-aspartate at 1.80… · 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 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
- Elsewhere: RCSB PDB 4O3A · PDBe 4O3A · UniProt P19491
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.