MolNFT v1 · #162410 · protein
Structure of arabidopsis thaliana GLR3.3 ligand-binding domain in complex with glycine
6R88 · Glutamate receptor 3.3,GLUTAMATE receptor 3.3: “Structure of arabidopsis thaliana GLR3.3 ligand-binding domain in complex with glycine”. X-ray diffraction, 4 ligands (GLY, NA, SO4), 9 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6R88
- Type
- protein
- Length
- 961 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
- GLY, NA, SO4, CL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 242 | 37% helix, 23% strand | Q9C8E7 |
| B, C | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 238 | 36% helix, 20% strand | Q9C8E7 |
| D | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 243 | 36% helix, 23% strand | Q9C8E7 |
Ligands and binding sites
- GLY · Glycine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains C, D
- CL · Chloride ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.85 | 0.86 | 125 | NA |
| 2 | 138 | 0.68 | 0.89 | 24 | empty |
| 3 | 351 | 0.56 | 0.75 | 41 | empty |
| 4 | 80 | 0.40 | 0.78 | 17 | empty |
| 5 | 58 | 0.38 | 0.79 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–D · 623 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 613 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 448 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6R88 · Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with glycine · 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 C 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 6R88 · PDBe 6R88 · UniProt Q9C8E7
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