MolNFT v1 · #65773 · protein
Crystal structure of the IGLUR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and cyclothiazide at 2.25 a resolution
3H6T · Glutamate receptor 2: “Crystal structure of the IGLUR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and cyclothiazide…”. X-ray diffraction, 3 ligands (GLU, CYZ, ZN), 8 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 3H6T
- Type
- protein
- Length
- 785 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, CYZ, ZN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 261 | 38% helix, 21% strand | P19491 |
| B | Glutamate receptor 2 | protein | 263 | 35% helix, 21% strand | P19491 |
| C | Glutamate receptor 2 | protein | 261 | 37% helix, 21% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
- CYZ · Cyclothiazide · ligand · 3 copies · chains A, C, B
- ZN · Zinc ion · metal · 10 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, C, B
- ACT · Acetate ion · additive · 2 copies · chains A, C
- DMS · Dimethyl sulfoxide · additive · chains A
- CAC · Cacodylate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.83 | 0.84 | 129 | CYZ, GOL |
| 2 | 54 | 0.72 | 0.99 | 19 | GLU |
| 3 | 232 | 0.54 | 0.78 | 33 | empty |
| 4 | 149 | 0.44 | 0.76 | 26 | empty |
| 5 | 81 | 0.38 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 920 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 322 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 79 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3H6T · Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with… · 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 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 P19491
- Elsewhere: RCSB PDB 3H6T · PDBe 3H6T · UniProt P19491
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