MolNFT v1 · #68876 · protein
Crystal structure of a E93K mutant of the majour bacillus subtilis glutamate dehydrogenase rocg
3K92 · NAD-specific glutamate dehydrogenase: “Crystal structure of a E93K mutant of the majour bacillus subtilis glutamate dehydrogenase rocg”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #68876 on GenesisL1: 3D…
- PDB
- 3K92
- Type
- protein
- Length
- 2,433 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-specific glutamate dehydrogenase
- EC
- 1.4.1.2
- UniProt
- P39633
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 418 | 51% helix, 16% strand | P39633 |
| B, C | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 409 | 49% helix, 16% strand | P39633 |
| D | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 406 | 50% helix, 15% strand | P39633 |
| E | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 396 | 50% helix, 14% strand | P39633 |
| F | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 395 | 47% helix, 15% strand | P39633 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, C, D, E, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.85 | 0.86 | 142 | empty |
| 2 | 880 | 0.83 | 0.85 | 75 | empty |
| 3 | 1099 | 0.83 | 0.84 | 126 | empty |
| 4 | 850 | 0.82 | 0.85 | 76 | empty |
| 5 | 819 | 0.82 | 0.85 | 72 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1015 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1015 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 997 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 884 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 875 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3K92 · Crystal structure of a E93K mutant of the majour Bacillus subtilis glutamate… · the same entry in another collection · chain F against F, TM-score 1.00
- P39633 · AlphaFold monomer V2.0 prediction for catabolic NAD-specific glutamate dehydrogenase rocg… · a predicted model of the same protein · 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 P39633
- Elsewhere: RCSB PDB 3K92 · PDBe 3K92 · UniProt P39633
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