MolNFT v1 · #62905 · protein
Crystal structure of bovine glutamate dehydrogenase complexed with hexachlorophene
3ETE: “Crystal structure of bovine glutamate dehydrogenase complexed with hexachlorophene”. X-ray diffraction, 4 ligands (GLU, NDP, GTP), 20 pockets (best druggability 0.89). MolNFT v1 #62905 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ETE
- Type
- protein
- Length
- 2,970 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- EC
- 1.4.1.3
- UniProt
- Q3SYY0
- Ligands
- GLU, NDP, GTP, H3P
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 495 | 47% helix, 14% strand | Q3SYY0 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, D, E, F
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- H3P · 2,2'-methanediylbis(3,4,6-trichlorophenol) · ligand · 6 copies · chains A, E, B, C, D, 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 | 1046 | 0.89 | 0.91 | 134 | empty |
| 2 | 1142 | 0.88 | 0.89 | 116 | empty |
| 3 | 1191 | 0.87 | 0.89 | 110 | empty |
| 4 | 1010 | 0.87 | 0.88 | 79 | empty |
| 5 | 1137 | 0.87 | 0.88 | 81 | empty |
Interfaces
12 interfaces between chains.
- C–E · 1875 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1866 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 1861 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1838 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1826 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3ETE · Crystal structure of bovine glutamate dehydrogenase complexed with hexachlorophene · 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 Q3SYY0
- Elsewhere: RCSB PDB 3ETE · PDBe 3ETE · UniProt Q3SYY0
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