Research workbench
Glutamate dehydrogenase in complex with NADH, closed conformation
Analyse Glutamate dehydrogenase in complex with NADH, closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JD1
- Type
- protein
- Length
- 2,976 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
- Ligands
- NAI
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 48% 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 | 496 | 48% helix, 14% strand | P00366 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 12 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.84 | 0.85 | 66 | empty |
| 2 | 1185 | 0.84 | 0.85 | 66 | empty |
| 3 | 890 | 0.83 | 0.85 | 76 | NAI |
| 4 | 879 | 0.82 | 0.85 | 78 | NAI |
| 5 | 846 | 0.82 | 0.85 | 68 | NAI |
Interfaces
15 interfaces between chains.
- B–C · 1871 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1870 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1868 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1868 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1866 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3JD1 · Glutamate dehydrogenase in complex with NADH, closed conformation · 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 B 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 P00366
- Elsewhere: RCSB PDB 3JD1 · PDBe 3JD1 · UniProt P00366
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