Research workbench
Crystal structure of arabidopsis thaliana glutamate-1-semialdehyde-2, 1-aminomutase
Analyse Crystal structure of arabidopsis thaliana glutamate-1-semialdehyde-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HDM
- Type
- protein
- Length
- 856 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplastic
- EC
- 5.4.3.8
- UniProt
- P42799
- Ligands
- PMP, PLP
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplastic (EC 5.4.3.8) | protein | 428 | 41% helix, 17% strand | P42799 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.75 | 0.82 | 66 | PMP |
| 2 | 76 | 0.75 | 0.98 | 24 | empty |
| 3 | 553 | 0.74 | 0.82 | 60 | PLP, PMP |
| 4 | 50 | 0.71 | 0.99 | 20 | empty |
| 5 | 50 | 0.69 | 0.98 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 4463 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5HDM · Crystal structure of Arabidopsis thaliana glutamate-1-semialdehyde-2,1-aminomutase · the same entry in another collection · chain A against A, TM-score 1.00
- P42799 · AlphaFold monomer V2.0 prediction for glutamate-1-semialdehyde 2,1-aminomutase 1… · a predicted model of the same protein · chain A 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 P42799
- Elsewhere: RCSB PDB 5HDM · PDBe 5HDM · UniProt P42799
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