MolNFT v1 · #86212 · protein
Structural basis of L-phosphoserine binding to bacillus alcalophilus phosphoserine aminotransferase
4AZJ: “Structural basis of L-phosphoserine binding to bacillus alcalophilus phosphoserine aminotransferase”. X-ray diffraction, 4 ligands (SEP, PLP, NA), 5 pockets (best druggability 0.71). MolNFT v1 #86212 on GenesisL1: 3D structure…
- PDB
- 4AZJ
- 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
- SEP, PLP, NA, CL
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine aminotransferase (EC 2.6.1.52) | protein | 360 | 41% helix, 17% strand | Q9RME2 |
| B | Phosphoserine aminotransferase (EC 2.6.1.52) | protein | 358 | 42% helix, 17% strand | Q9RME2 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
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 | 389 | 0.71 | 0.83 | 64 | SEP, PLP, NA |
| 2 | 363 | 0.68 | 0.81 | 54 | SEP, PLP, NA |
| 3 | 166 | 0.51 | 0.78 | 25 | empty |
| 4 | 124 | 0.43 | 0.76 | 23 | empty |
| 5 | 116 | 0.38 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2407 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4AZJ · 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 4AZJ · PDBe 4AZJ · UniProt Q9RME2
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