Research workbench
Glutamate dehydrogenase from thermococcus profundus in the unligated state
Analyse Glutamate dehydrogenase from thermococcus profundus in the unligated state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EUZ
- Type
- protein
- Length
- 2,497 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- EC
- 1.4.1.2
- UniProt
- O74024
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glutamate dehydrogenase (EC 1.4.1.2) | protein | 416 | 48% helix, 17% strand | O74024 |
| F | Glutamate dehydrogenase (EC 1.4.1.2) | protein | 417 | 49% helix, 17% strand | O74024 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.89 | 0.92 | 63 | empty |
| 2 | 837 | 0.89 | 0.92 | 57 | empty |
| 3 | 832 | 0.89 | 0.92 | 64 | empty |
| 4 | 976 | 0.83 | 0.84 | 100 | empty |
| 5 | 882 | 0.76 | 0.80 | 78 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1084 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1051 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 1036 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 993 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 972 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1EUZ · Glutamate dehydrogenase from thermococcus profundus in the unligated state · the same entry in another collection · chain F against F, TM-score 1.00
- O74024 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase (O74024) · a predicted model of the same protein · chain D against A, TM-score 1.00
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 1EUZ · PDBe 1EUZ · UniProt O74024
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