Research workbench
Arabidopsis thaliana glutamate dehydrogenase isoform 1 in apo form
Analyse Arabidopsis thaliana glutamate dehydrogenase isoform 1 in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YEH
- Type
- protein
- Length
- 2,455 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase 1
- EC
- 1.4.1.3
- UniProt
- Q43314
- Ligands
- K
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Glutamate dehydrogenase 1 (EC 1.4.1.3) | protein | 410 | 47% helix, 18% strand | Q43314 |
| B | Glutamate dehydrogenase 1 (EC 1.4.1.3) | protein | 409 | 49% helix, 18% strand | Q43314 |
| C, F | Glutamate dehydrogenase 1 (EC 1.4.1.3) | protein | 408 | 48% helix, 18% strand | Q43314 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.87 | 0.89 | 99 | K |
| 2 | 1068 | 0.87 | 0.89 | 96 | K |
| 3 | 1127 | 0.87 | 0.89 | 94 | K |
| 4 | 963 | 0.86 | 0.87 | 114 | empty |
| 5 | 906 | 0.85 | 0.87 | 109 | MPD |
Interfaces
13 interfaces between chains.
- A–B · 1214 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1202 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1190 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 856 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 850 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6YEH · Arabidopsis thaliana glutamate dehydrogenase isoform 1 in apo form · the same entry in another collection · chain F against F, TM-score 1.00
- Q43314 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase 1 (Q43314) · a predicted model of the same protein · chain C 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 Q43314
- Elsewhere: RCSB PDB 6YEH · PDBe 6YEH · UniProt Q43314
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