Research workbench
Crystal structure of GUDB1 a decryptified secondary glutamate dehydrogenase from B. subtilis
Analyse Crystal structure of GUDB1 a decryptified secondary glutamate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K8Z
- Type
- protein
- Length
- 2,354 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
- P50735
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 378 | 49% helix, 16% strand | P50735 |
| B, E | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 392 | 50% helix, 16% strand | P50735 |
| C, F | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 407 | 49% helix, 16% strand | P50735 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.89 | 0.94 | 74 | empty |
| 2 | 669 | 0.89 | 0.94 | 75 | empty |
| 3 | 643 | 0.88 | 0.94 | 76 | empty |
| 4 | 991 | 0.85 | 0.86 | 132 | empty |
| 5 | 1014 | 0.85 | 0.86 | 126 | empty |
Interfaces
12 interfaces between chains.
- D–F · 1185 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1181 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 1101 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 888 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 885 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3K8Z · Crystal Structure of Gudb1 a decryptified secondary glutamate dehydrogenase from B.… · the same entry in another collection · chain F against F, TM-score 1.00
- P50735 · AlphaFold monomer V2.0 prediction for cryptic catabolic NAD-specific glutamate… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P50735
- Elsewhere: RCSB PDB 3K8Z · PDBe 3K8Z · UniProt P50735
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