MolNFT v1 · #52706 · protein
Spt with plp, N100C
2W8T · Serine palmitoyltransferase: “Spt with plp, N100C”. X-ray diffraction, 1 ligand (PLP), 4 pockets (best druggability 0.52). MolNFT v1 #52706 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2W8T
- Type
- protein
- Length
- 397 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine palmitoyltransferase
- UniProt
- Q93UV0
- Ligands
- PLP
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine palmitoyltransferase | protein | 397 | 42% helix, 18% strand | Q93UV0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.52 | 0.78 | 42 | PLP |
| 2 | 75 | 0.38 | 0.77 | 20 | empty |
| 3 | 66 | 0.36 | 0.78 | 17 | empty |
| 4 | 73 | 0.30 | 0.73 | 18 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2W8T · SPT with PLP, N100C · 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 Q93UV0
- Elsewhere: RCSB PDB 2W8T · PDBe 2W8T · UniProt Q93UV0
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