Research workbench
Crystal structure of aspergillus terreus glutamate dehydrogenase (atgdh) complexed with tartrate 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
- 7ECT
- Type
- protein
- Length
- 1,378 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- UniProt
- T2D1F5
- Ligands
- NDP
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate dehydrogenase | protein | 459 | 48% helix, 15% strand | T2D1F5 |
| C | Glutamate dehydrogenase | protein | 460 | 48% helix, 14% strand | T2D1F5 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 12 copies · chains A, B, C
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.79 | 0.83 | 72 | NDP, GOL, TLA |
| 2 | 710 | 0.78 | 0.83 | 72 | NDP, GOL, TLA |
| 3 | 778 | 0.78 | 0.83 | 86 | NDP, TLA |
| 4 | 731 | 0.76 | 0.81 | 92 | GOL |
| 5 | 103 | 0.37 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1049 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1040 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7ECT · 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 7ECT · PDBe 7ECT · UniProt T2D1F5
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