Research workbench
Spt with plp-ser
Analyse Spt with plp-ser in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W8J
- Type
- protein
- Length
- 398 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine palmitoyltransferase
- UniProt
- Q93UV0
- Ligands
- PLS
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine palmitoyltransferase | protein | 398 | 42% helix, 17% strand | Q93UV0 |
Ligands and binding sites
- PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.55 | 0.84 | 20 | empty |
| 2 | 136 | 0.51 | 0.80 | 22 | empty |
| 3 | 196 | 0.50 | 0.77 | 28 | PLS |
| 4 | 77 | 0.37 | 0.76 | 17 | empty |
| 5 | 64 | 0.29 | 0.74 | 16 | empty |
Compared structures
- 2W8J · SPT with PLP-ser · 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 2W8J · PDBe 2W8J · UniProt Q93UV0
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