MolNFT v1 · #162411 · protein
Structure of arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-cysteine
6R89 · Glutamate receptor 3.3,GLUTAMATE receptor 3.3: “Structure of arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-cysteine”. X-ray diffraction, 3 ligands (CYS, NA, CL), 11 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 6R89
- Type
- protein
- Length
- 960 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
- CYS, NA, CL
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 242 | 36% helix, 20% strand | Q9C8E7 |
| B, C | Glutamate receptor 3.3,GLUTAMATE receptor 3.3 | protein | 238 | 37% helix, 20% strand | Q9C8E7 |
Ligands and binding sites
- CYS · Cysteine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.80 | 0.86 | 60 | CL |
| 2 | 353 | 0.77 | 0.88 | 55 | empty |
| 3 | 200 | 0.69 | 0.86 | 25 | empty |
| 4 | 170 | 0.68 | 0.87 | 27 | empty |
| 5 | 330 | 0.55 | 0.75 | 41 | empty |
Interfaces
6 interfaces between chains.
- B–D · 637 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 601 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 479 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 421 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 276 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6R89 · Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-cysteine · 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 6R89 · PDBe 6R89 · UniProt Q9C8E7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.