Research workbench
Cryo-EM structure of glutamate dehydrogenase from thermococcus profundus
Analyse Cryo-EM structure of glutamate dehydrogenase from thermococcus profundus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JND
- Type
- protein
- Length
- 419 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- EC
- 1.4.1.3
- UniProt
- O74024
- Pockets
- 3 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 419 | 41% helix, 14% strand | O74024 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.75 | 0.80 | 57 | TRS |
| 2 | 75 | 0.51 | 0.85 | 14 | empty |
| 3 | 55 | 0.34 | 0.78 | 14 | empty |
Compared structures
- 6JND · Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus · the same entry in another collection · chain A against A, TM-score 1.00
- O74024 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase (O74024) · a predicted model of the same protein · chain A 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 O74024
- Elsewhere: RCSB PDB 6JND · PDBe 6JND · UniProt O74024
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