MolNFT v1 · #162412 · protein
Structure of arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-methionine
6R8A · Glutamate receptor 3.3,GLUTAMATE receptor 3.3: “Structure of arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-methionine”. X-ray diffraction, 3 ligands (MET, NA, SO4), 12 pockets (best druggability 0.77). MolNFT…
- PDB
- 6R8A
- Type
- protein
- Length
- 920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 3.3,GLUTAMATE receptor 3.3
- UniProt
- Q9C8E7
- Ligands
- MET, NA, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 237 | 35% helix, 23% strand | Q9C8E7 |
| B | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 209 | 35% helix, 18% strand | Q9C8E7 |
| D | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 237 | 35% helix, 23% strand | Q9C8E7 |
Ligands and binding sites
- MET · Methionine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.77 | 0.83 | 55 | empty |
| 2 | 303 | 0.64 | 0.81 | 32 | empty |
| 3 | 274 | 0.60 | 0.79 | 34 | empty |
| 4 | 138 | 0.50 | 0.79 | 28 | empty |
| 5 | 154 | 0.49 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 554 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 449 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 406 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 269 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 159 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6R8A · Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9C8E7 · AlphaFold monomer V2.0 prediction for glutamate receptor 3.3 (Q9C8E7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9C8E7
- Elsewhere: RCSB PDB 6R8A · PDBe 6R8A · UniProt Q9C8E7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.