MolNFT v1 · #140753 · protein
Crystal structure of a glutamate-1-semialdehyde-aminomutase (K286A) from pseudomonas aeruginosa PAO1 in complex with pmp
5YKT · Probable aminotransferase: “Crystal structure of a glutamate-1-semialdehyde-aminomutase (K286A) from pseudomonas aeruginosa PAO1 in…”. X-ray diffraction, 1 ligand (PMP), 6 pockets (best druggability 0.81). MolNFT v1 #140753 on…
- PDB
- 5YKT
- Type
- protein
- Length
- 906 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable aminotransferase
- EC
- 5.4.3.8
- UniProt
- Q9HWU0
- Ligands
- PMP
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable aminotransferase (EC 5.4.3.8) | protein | 453 | 44% helix, 16% strand | Q9HWU0 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.81 | 0.89 | 56 | PMP, GOL |
| 2 | 449 | 0.81 | 0.88 | 58 | PMP, GOL |
| 3 | 153 | 0.76 | 0.94 | 34 | empty |
| 4 | 50 | 0.70 | 0.98 | 21 | empty |
| 5 | 60 | 0.53 | 0.88 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 5751 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 5YKT · Crystal structure of a glutamate-1-semialdehyde-aminomutase (K286A) from Pseudomonas… · the same entry in another collection · chain A 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 Q9HWU0
- Elsewhere: RCSB PDB 5YKT · PDBe 5YKT · UniProt Q9HWU0
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