Research workbench
Cryo-EM structure of glutamate dehydrogenase at 1.8 a resolution
Analyse Cryo-EM structure of glutamate dehydrogenase at 1.8 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K12
- Type
- protein
- Length
- 1,764 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase 1, mitochondrial
- EC
- 1.4.1.3
- UniProt
- P00366
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate dehydrogenase 1, mitochondrial (EC 1.4.1.3) | protein | 294 | 50% helix, 14% strand | P00366 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.87 | 0.92 | 40 | empty |
| 2 | 554 | 0.87 | 0.92 | 39 | empty |
| 3 | 962 | 0.81 | 0.83 | 88 | empty |
| 4 | 720 | 0.80 | 0.85 | 77 | empty |
| 5 | 584 | 0.79 | 0.85 | 67 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1651 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 1646 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1645 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 1644 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1642 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5K12 · Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution · the same entry in another collection · chain F against F, TM-score 1.00
- P00366 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase 1, mitochondrial (P00366) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P00366
- Elsewhere: RCSB PDB 5K12 · PDBe 5K12 · UniProt P00366
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