Research workbench
Bovine glutamate dehydrogenase complexed with EU3+
Analyse Bovine glutamate dehydrogenase complexed with EU3+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DHN
- Type
- protein
- Length
- 3,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase 1, mitochondrial
- EC
- 1.4.1.2
- UniProt
- A0A140T871
- Ligands
- NAI, GLU, GTP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate dehydrogenase 1, mitochondrial (EC 1.4.1.2) | protein | 501 | 49% helix, 12% strand | A0A140T871 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F
- GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, D, E, F
- 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 | 796 | 0.88 | 0.91 | 66 | empty |
| 2 | 778 | 0.87 | 0.90 | 65 | empty |
| 3 | 736 | 0.83 | 0.87 | 76 | NAI |
| 4 | 830 | 0.83 | 0.86 | 77 | NAI |
| 5 | 857 | 0.83 | 0.85 | 80 | NAI |
Interfaces
15 interfaces between chains.
- B–C · 2051 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 2025 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1987 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1981 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1939 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6DHN · Bovine glutamate dehydrogenase complexed with Eu3+ · the same entry in another collection · chain A 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 A0A140T871
- Elsewhere: RCSB PDB 6DHN · PDBe 6DHN · UniProt A0A140T871
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