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Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Malonate and NADPH
Analyse Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ECS
- Type
- protein
- Length
- 1,380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.74
- Source
- Aspergillus terreus
- Molecule
- Glutamate dehydrogenase
- UniProt
- T2D1F5
- Ligands
- NDP
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.74 · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate dehydrogenase | protein | 460 | 47% helix, 15% strand | T2D1F5 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 24 copies · chains A, C, B
- MLI · Malonate ion · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.79 | 0.84 | 71 | MLI, NDP |
| 2 | 760 | 0.78 | 0.83 | 77 | MLI, NDP |
| 3 | 730 | 0.78 | 0.83 | 73 | GOL, MLI, NDP |
| 4 | 623 | 0.76 | 0.82 | 77 | empty |
| 5 | 130 | 0.45 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1027 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1015 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 994 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7ECS · Crystal structure of aspergillus terreus glutamate dehydrogenase (atgdh) complexed with… · 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 T2D1F5
- Elsewhere: RCSB PDB 7ECS · PDBe 7ECS · UniProt T2D1F5
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