Research workbench
Crystal structure of glutamate-1-semialdehyde 2,1- aminomutase from aeropyrum pernix, hexagonal form
Analyse Crystal structure of glutamate-1-semialdehyde 2,1- aminomutase from aeropyrum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZSM
- Type
- protein
- Length
- 1,263 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate-1-semialdehyde 2,1-aminomutase
- EC
- 5.4.3.8
- UniProt
- Q9Y9I9
- Ligands
- PMP, CL
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 425 | 43% helix, 18% strand | Q9Y9I9 |
| B, C | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 419 | 44% helix, 18% strand | Q9Y9I9 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.78 | 0.99 | 21 | empty |
| 2 | 51 | 0.74 | 0.99 | 14 | empty |
| 3 | 486 | 0.72 | 0.81 | 62 | PMP |
| 4 | 446 | 0.72 | 0.82 | 58 | PMP |
| 5 | 631 | 0.68 | 0.77 | 78 | PMP, CL |
Interfaces
2 interfaces between chains.
- B–C · 4632 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 735 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2ZSM · Crystal structure of glutamate-1-semialdehyde 2,1-aminomutase from Aeropyrum pernix… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y9I9 · AlphaFold monomer V2.0 prediction for glutamate-1-semialdehyde 2,1-aminomutase (Q9Y9I9) · a predicted model of the same protein · chain B 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 Q9Y9I9
- Elsewhere: RCSB PDB 2ZSM · PDBe 2ZSM · UniProt Q9Y9I9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.