MolNFT v1 · #162409 · protein
Structure of arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-glutamate
6R85 · Glutamate receptor 3.3,GLUTAMATE receptor 3.3: “Structure of arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-glutamate”. X-ray diffraction, 3 ligands (GLU, NA, SO4), 4 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 6R85
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 3.3,GLUTAMATE receptor 3.3
- UniProt
- Q9C8E7
- Ligands
- GLU, NA, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 238 | 37% helix, 23% strand | Q9C8E7 |
| B | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 239 | 36% helix, 20% strand | Q9C8E7 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.73 | 0.78 | 89 | SO4 |
| 2 | 60 | 0.33 | 0.76 | 18 | EDO |
| 3 | 62 | 0.31 | 0.75 | 17 | empty |
| 4 | 81 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 793 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6R85 · Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-glutamate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9C8E7 · AlphaFold monomer V2.0 prediction for glutamate receptor 3.3 (Q9C8E7) · a predicted model of the same protein · chain B 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 Q9C8E7
- Elsewhere: RCSB PDB 6R85 · PDBe 6R85 · UniProt Q9C8E7
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