MolNFT v1 · #146440 · protein
Bovine glutamate dehydrogenase complexed with epicatechin-3-gallate (ecg)
6DHL · Glutamate dehydrogenase 1, mitochondrial: “Bovine glutamate dehydrogenase complexed with epicatechin-3-gallate (ecg)”. X-ray diffraction, 1 ligand (XEG), 20 pockets (best druggability 0.86). MolNFT v1 #146440 on GenesisL1: 3D…
- PDB
- 6DHL
- 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
- XEG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 12% 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 | 45% helix, 12% strand | A0A140T871 |
Ligands and binding sites
- XEG · (2R,3S)-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate · ligand · 12 copies · chains A, F, B, C, D, E, G, L, H, 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 | 733 | 0.86 | 0.89 | 52 | empty |
| 2 | 685 | 0.86 | 0.90 | 47 | empty |
| 3 | 613 | 0.86 | 0.90 | 39 | empty |
| 4 | 788 | 0.86 | 0.88 | 58 | empty |
| 5 | 1102 | 0.85 | 0.86 | 109 | XEG |
Interfaces
32 interfaces between chains.
- C–E · 2094 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 2085 Ų buried · 21 hydrogen bonds · protein-protein
- G–L · 2067 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2065 Ų buried · 17 hydrogen bonds · protein-protein
- I–K · 2050 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6DHL · Bovine glutamate dehydrogenase complexed with epicatechin-3-gallate (ECG) · 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 6DHL · PDBe 6DHL · UniProt A0A140T871
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