MolNFT v1 · #15228 · protein
Crystal structure of glutamate receptor ligand-binding core in complex with bromo-willardiine in the zn crystal form
1MY3 · Glutamate receptor 2: “Crystal structure of glutamate receptor ligand-binding core in complex with bromo-willardiine in the zn…”. X-ray diffraction, 2 ligands (BWD, ZN), 10 pockets (best druggability 0.80). MolNFT v1 #15228 on…
- PDB
- 1MY3
- Type
- protein
- Length
- 775 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- BWD, ZN
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 2 | protein | 258 | 38% helix, 21% strand | P19491 |
| B | Glutamate receptor 2 | protein | 259 | 36% helix, 21% strand | P19491 |
Ligands and binding sites
- BWD · 2-amino-3-(5-bromo-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-propionic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.80 | 0.85 | 100 | empty |
| 2 | 60 | 0.72 | 0.98 | 21 | BWD |
| 3 | 58 | 0.71 | 0.98 | 21 | BWD |
| 4 | 56 | 0.69 | 0.97 | 19 | BWD |
| 5 | 311 | 0.64 | 0.80 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–C · 903 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 331 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1MY3 · crystal structure of glutamate receptor ligand-binding core in complex with… · 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 1MY3 · PDBe 1MY3 · UniProt P19491
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