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Crystal structure of glutamate-1-semialdehyde 2,1- aminomutase (gsa) from pseudomonas aeruginosa
Analyse Crystal structure of glutamate-1-semialdehyde 2,1- aminomutase (gsa) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I92
- Type
- protein
- Length
- 2,530 residues
- Chains
- 6
- 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
- P48247
- Ligands
- LEU
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 424 | 42% helix, 18% strand | P48247 |
| B | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 421 | 42% helix, 18% strand | P48247 |
| C, E | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 421 | 43% helix, 18% strand | P48247 |
| D | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 423 | 42% helix, 18% strand | P48247 |
| F | Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) | protein | 420 | 42% helix, 18% strand | P48247 |
Ligands and binding sites
- LEU · Leucine · ligand · chains F
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.83 | 0.85 | 84 | GOL |
| 2 | 910 | 0.82 | 0.84 | 90 | empty |
| 3 | 814 | 0.81 | 0.84 | 84 | empty |
| 4 | 845 | 0.81 | 0.84 | 93 | GOL |
| 5 | 778 | 0.81 | 0.84 | 78 | EDO |
Interfaces
10 interfaces between chains.
- A–B · 4333 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 4313 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 4209 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 724 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 288 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5I92 · Crystal structure of Glutamate-1-semialdehyde 2,1- aminomutase (GSA) from Pseudomonas… · the same entry in another collection · chain F against F, TM-score 1.00
- P48247 · AlphaFold monomer V2.0 prediction for glutamate-1-semialdehyde 2,1-aminomutase (P48247) · a predicted model of the same protein · chain B 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 P48247
- Elsewhere: RCSB PDB 5I92 · PDBe 5I92 · UniProt P48247
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