MolNFT v1 · #15229 · protein
Crystal structure of glutamate receptor ligand-binding core in complex with iodo-willardiine in the zn crystal form
1MY4 · Glutamate receptor 2: “Crystal structure of glutamate receptor ligand-binding core in complex with iodo-willardiine in the zn…”. X-ray diffraction, 2 ligands (IWD, ZN), 12 pockets (best druggability 0.72). MolNFT v1 #15229 on…
- PDB
- 1MY4
- 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
- IWD, ZN
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 2 | protein | 258 | 39% helix, 21% strand | P19491 |
| B | Glutamate receptor 2 | protein | 259 | 37% helix, 21% strand | P19491 |
Ligands and binding sites
- IWD · 2-amino-3-(5-iodo-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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.72 | 0.84 | 56 | empty |
| 2 | 261 | 0.72 | 0.86 | 42 | empty |
| 3 | 56 | 0.72 | 0.98 | 19 | IWD |
| 4 | 61 | 0.71 | 0.97 | 21 | IWD |
| 5 | 62 | 0.71 | 0.97 | 20 | IWD |
Interfaces
3 interfaces between chains.
- A–C · 925 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 242 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1MY4 · 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 1MY4 · PDBe 1MY4 · UniProt P19491
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