Research workbench
Glutamate dehydrogenase in complex with NADH and GTP, closed conformation
Analyse Glutamate dehydrogenase in complex with NADH and GTP, closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JD4
- Type
- protein
- Length
- 2,982 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, GTP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 48% helix, 12% 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 | 497 | 48% helix, 12% strand | P00366 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 12 copies · chains A, C, B, D, F, E
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
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 | 867 | 0.87 | 0.89 | 81 | empty |
| 2 | 846 | 0.87 | 0.89 | 75 | empty |
| 3 | 740 | 0.83 | 0.87 | 69 | NAI |
| 4 | 765 | 0.82 | 0.86 | 71 | NAI |
| 5 | 739 | 0.82 | 0.86 | 63 | NAI |
Interfaces
15 interfaces between chains.
- A–C · 1905 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1901 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1896 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1892 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1891 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3JD4 · Glutamate dehydrogenase in complex with NADH and GTP, 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 A 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 3JD4 · PDBe 3JD4 · UniProt P00366
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