Research workbench
Structural basis of L-phosphoserine binding to bacillus alcalophilus phosphoserine aminotransferase
Analyse Structural basis of L-phosphoserine binding to bacillus alcalophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AZK
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine aminotransferase
- EC
- 2.6.1.52
- UniProt
- Q9RME2
- Ligands
- PLP, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine aminotransferase (EC 2.6.1.52) | protein | 360 | 39% helix, 17% strand | Q9RME2 |
| B | Phosphoserine aminotransferase (EC 2.6.1.52) | protein | 358 | 42% helix, 17% strand | Q9RME2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.66 | 0.78 | 54 | PLP |
| 2 | 364 | 0.63 | 0.79 | 50 | PLP |
| 3 | 160 | 0.51 | 0.78 | 24 | empty |
| 4 | 133 | 0.43 | 0.76 | 23 | empty |
| 5 | 159 | 0.41 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2306 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4AZK · Structural basis of L-phosphoserine binding to Bacillus alcalophilus phosphoserine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RME2 · AlphaFold monomer V2.0 prediction for phosphoserine aminotransferase (Q9RME2) · 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 Q9RME2
- Elsewhere: RCSB PDB 4AZK · PDBe 4AZK · UniProt Q9RME2
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