MolNFT v1 · #32177 · protein
Radiation damage of the schiff base in phosphoserine aminotransferase (structure I)
2BIG: “Radiation damage of the schiff base in phosphoserine aminotransferase (structure I)”. X-ray diffraction, 3 ligands (PLP, MG, CL), 5 pockets (best druggability 0.68). MolNFT v1 #32177 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2BIG
- Type
- protein
- Length
- 713 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, MG, CL
- Pockets
- 5 · best druggability 0.68
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 | 358 | 41% helix, 17% strand | Q9RME2 |
| B | Phosphoserine aminotransferase (EC 2.6.1.52) | protein | 355 | 41% helix, 17% strand | Q9RME2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.68 | 0.80 | 54 | PLP, CL |
| 2 | 330 | 0.67 | 0.82 | 57 | PLP, CL |
| 3 | 152 | 0.49 | 0.78 | 22 | empty |
| 4 | 174 | 0.44 | 0.74 | 24 | empty |
| 5 | 126 | 0.43 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2301 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2BIG · Radiation damage of the Schiff base in phosphoserine aminotransferase (structure I) · 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 2BIG · PDBe 2BIG · UniProt Q9RME2
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