MolNFT v1 · #111282 · protein
Structure of the ligand-binding domain of GLUA2 in complex with the antagonist CNG10109
4YMA · Glutamate receptor 2: “Structure of the ligand-binding domain of GLUA2 in complex with the antagonist CNG10109”. X-ray diffraction, 2 ligands (4E5, SO4), 4 pockets (best druggability 0.81). MolNFT v1 #111282 on GenesisL1: 3D…
- PDB
- 4YMA
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- 4E5, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glutamate receptor 2 | protein | 260 | 38% helix, 20% strand | P19491 |
| A | Glutamate receptor 2 | protein | 258 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- 4E5 · (3R)-3-(3-carboxy-5-hydroxyphenyl)-L-proline · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 6 copies · chains B, A
- GOL · Glycerol · additive · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- ACT · Acetate ion · additive · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.81 | 0.82 | 124 | SO4, 4E5, ACT |
| 2 | 268 | 0.59 | 0.79 | 32 | empty |
| 3 | 80 | 0.42 | 0.79 | 24 | empty |
| 4 | 126 | 0.41 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- B–A · 1002 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4YMA · Structure of the ligand-binding domain of GluA2 in complex with the antagonist CNG10109 · the same entry in another collection · chain A against A, 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 0.96
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 4YMA · PDBe 4YMA · UniProt P19491
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