Research workbench
Structure of glutamate dehydrogenase complexed with bithionol
Analyse Structure of glutamate dehydrogenase complexed with bithionol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ETD
- Type
- protein
- Length
- 3,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Bos taurus
- Molecule
- GLUD1 protein
- UniProt
- Q3SYY0
- Ligands
- GLU, NDP, GTP, B1T
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 2.5 · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | GLUD1 protein | protein | 501 | 48% 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
- B1T · 2,2'-sulfanediylbis(4,6-dichlorophenol) · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.89 | 0.92 | 138 | B1T |
| 2 | 1159 | 0.89 | 0.90 | 120 | B1T |
| 3 | 1032 | 0.87 | 0.88 | 77 | empty |
| 4 | 1034 | 0.87 | 0.88 | 77 | empty |
| 5 | 366 | 0.83 | 0.92 | 58 | empty |
Interfaces
15 interfaces between chains.
- A–F · 1922 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1913 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 1892 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1884 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1872 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3ETD · Structure of glutamate dehydrogenase complexed with bithionol · 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 3ETD · PDBe 3ETD · UniProt Q3SYY0
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