Research workbench
Crystal structure of hetero-hexameric glutamate dehydrogenase from thermus thermophilus (leu bound form)
Analyse Crystal structure of hetero-hexameric glutamate dehydrogenase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AOE
- Type
- protein
- Length
- 2,512 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- EC
- 1.4.1.3
- UniProt
- Q72IC1, Q72IC0
- Ligands
- LEU
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 422 | 47% helix, 16% strand | Q72IC1 |
| B | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 424 | 47% helix, 17% strand | Q72IC1 |
| E, D | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 416 | 48% helix, 18% strand | Q72IC0 |
| F, C | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 417 | 48% helix, 17% strand | Q72IC0 |
Ligands and binding sites
- LEU · Leucine · ligand · 6 copies · chains A, B, C, F, E, D
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 | 1066 | 0.81 | 0.82 | 94 | empty |
| 2 | 168 | 0.80 | 0.96 | 21 | LEU |
| 3 | 158 | 0.80 | 0.97 | 22 | LEU |
| 4 | 725 | 0.80 | 0.84 | 90 | empty |
| 5 | 859 | 0.79 | 0.82 | 73 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1883 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1425 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1386 Ų buried · 16 hydrogen bonds · protein-protein
- F–D · 1073 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 1030 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3AOE · Crystal structure of hetero-hexameric glutamate dehydrogenase from Thermus thermophilus… · 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 Q72IC1
- Every structure of UniProt Q72IC0
- Elsewhere: RCSB PDB 3AOE · PDBe 3AOE · UniProt Q72IC1 · UniProt Q72IC0
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