Research workbench
Crystal structure of a glutamate-1-semialdehyde aminotransferase from bacillus anthracis with bound pyridoxal 5'PHOSPHATE
Analyse Crystal structure of a glutamate-1-semialdehyde aminotransferase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K28
- Type
- protein
- Length
- 1,687 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate-1-semialdehyde 2,1-aminomutase 2
- EC
- 5.4.3.8
- UniProt
- Q81LD0
- Ligands
- PLP, CA, CL
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate-1-semialdehyde 2,1-aminomutase 2 (EC 5.4.3.8) | protein | 423 | 43% helix, 16% strand | Q81LD0 |
| B, C | Glutamate-1-semialdehyde 2,1-aminomutase 2 (EC 5.4.3.8) | protein | 422 | 43% helix, 16% strand | Q81LD0 |
| D | Glutamate-1-semialdehyde 2,1-aminomutase 2 (EC 5.4.3.8) | protein | 420 | 43% helix, 16% strand | Q81LD0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.81 | 0.93 | 50 | PLP |
| 2 | 550 | 0.80 | 0.87 | 65 | empty |
| 3 | 307 | 0.79 | 0.90 | 54 | PLP, CA |
| 4 | 505 | 0.78 | 0.85 | 63 | empty |
| 5 | 279 | 0.78 | 0.90 | 56 | PLP, CA |
Interfaces
5 interfaces between chains.
- A–B · 4675 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 4631 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 497 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 457 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 178 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified, 4 cofactor (engineered, pyridoxal phosphate Schiff base).
Compared structures
- 3K28 · Crystal Structure of a glutamate-1-semialdehyde aminotransferase from Bacillus anthracis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q81LD0 · AlphaFold monomer V2.0 prediction for glutamate-1-semialdehyde 2,1-aminomutase 2 (Q81LD0) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q81LD0
- Elsewhere: RCSB PDB 3K28 · PDBe 3K28 · UniProt Q81LD0
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