Research workbench
Bovine glutamate dehydrogenase complexed with ADP
Analyse Bovine glutamate dehydrogenase complexed with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DHK
- Type
- protein
- Length
- 5,952 residues
- Chains
- 12
- 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
- ADP
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Glutamate dehydrogenase 1, mitochondrial (EC 1.4.1.2) | protein | 496 | 44% helix, 15% strand | A0A140T871 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, B, F, C, D, E, G, H, L, I, J, K
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 | 1106 | 0.91 | 0.93 | 131 | ADP |
| 2 | 1046 | 0.91 | 0.93 | 134 | ADP |
| 3 | 1120 | 0.90 | 0.92 | 118 | ADP |
| 4 | 1142 | 0.89 | 0.91 | 115 | ADP |
| 5 | 875 | 0.89 | 0.92 | 93 | empty |
Interfaces
38 interfaces between chains.
- D–E · 2066 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 2045 Ų buried · 28 hydrogen bonds · protein-protein
- I–K · 2029 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 2006 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 2004 Ų buried · 21 hydrogen bonds · protein-protein
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 6DHK · PDBe 6DHK · UniProt A0A140T871
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