MolNFT v1 · #141689 · protein
Crystal structure of the GLUA2O lbd in complex with glutamate and tak- 137
5ZG3 · Glutamate receptor 2: “Crystal structure of the GLUA2O lbd in complex with glutamate and tak- 137”. X-ray diffraction, 3 ligands (GLU, 9C6, ZN), 13 pockets (best druggability 0.83). MolNFT v1 #141689 on GenesisL1: 3D structure…
- PDB
- 5ZG3
- 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, 9C6, ZN
- Pockets
- 13 · 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
- 9C6 · 9-(4-phenoxyphenyl)-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 B, A, C, D, E, F
- ACT · Acetate ion · additive · 11 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.83 | 0.84 | 129 | 9C6, ACT |
| 2 | 1140 | 0.82 | 0.83 | 130 | ACT, 9C6 |
| 3 | 629 | 0.82 | 0.86 | 101 | 9C6 |
| 4 | 60 | 0.52 | 0.87 | 24 | empty |
| 5 | 74 | 0.50 | 0.85 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1046 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1038 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 991 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 355 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 318 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5ZG3 · Crystal structure of the GluA2o LBD in complex with glutamate and TAK-137 · 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 E 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 5ZG3 · PDBe 5ZG3 · UniProt P42262
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