MolNFT v1 · #141686 · protein
Crystal structure of the GLUA2O lbd in complex with glutamate and compound-1
5ZG0 · Glutamate receptor 2: “Crystal structure of the GLUA2O lbd in complex with glutamate and compound-1”. X-ray diffraction, 3 ligands (GLU, 9C3, ZN), 15 pockets (best druggability 0.83). MolNFT v1 #141686 on GenesisL1: 3D structure…
- PDB
- 5ZG0
- Type
- protein
- Length
- 1,562 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P42262
- Ligands
- GLU, 9C3, ZN
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Glutamate receptor 2 | protein | 260 | 38% helix, 21% strand | P42262 |
| D | Glutamate receptor 2 | protein | 262 | 36% helix, 21% strand | P42262 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, D, E, F
- 9C3 · 9-{4-[(propan-2-yl)oxy]phenyl}-3,4-dihydro-2H-2lambda~6~-pyrido[2,1-c][1,2,4]thiadiazine-2,2-dione · ligand · 3 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 12 copies · chains A, C, B, D, E, F
- ACT · Acetate ion · additive · 7 copies · chains C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.83 | 0.84 | 131 | 9C3, ACT |
| 2 | 1171 | 0.82 | 0.83 | 135 | ACT, 9C3 |
| 3 | 616 | 0.79 | 0.84 | 84 | 9C3, ACT |
| 4 | 93 | 0.54 | 0.85 | 28 | empty |
| 5 | 76 | 0.53 | 0.86 | 23 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1074 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1044 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1040 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 316 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5ZG0 · Crystal structure of the GluA2o LBD in complex with glutamate and Compound-1 · the same entry in another collection · chain F against F, TM-score 1.00
- P42262 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P42262) · a predicted model of the same protein · chain A 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 P42262
- Elsewhere: RCSB PDB 5ZG0 · PDBe 5ZG0 · UniProt P42262
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.