MolNFT v1 · #86964 · protein
Serine palmitoyltransferase K265A from S. paucimobilis with bound plp-myriocin aldimine
4BMK: “Serine palmitoyltransferase K265A from S. paucimobilis with bound plp-myriocin aldimine”. X-ray diffraction, 2 ligands (PLP, MYB), 8 pockets (best druggability 0.83). MolNFT v1 #86964 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4BMK
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine palmitoyltransferase
- EC
- 2.3.1.50
- UniProt
- Q93UV0
- Ligands
- PLP, MYB
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine palmitoyltransferase (EC 2.3.1.50) | protein | 398 | 42% helix, 18% strand | Q93UV0 |
| B | Serine palmitoyltransferase (EC 2.3.1.50) | protein | 386 | 43% helix, 17% strand | Q93UV0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MYB · Decarboxylated Myriocin · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.83 | 0.90 | 61 | PLP, MYB |
| 2 | 519 | 0.75 | 0.83 | 57 | PLP, MYB |
| 3 | 122 | 0.46 | 0.78 | 23 | empty |
| 4 | 100 | 0.45 | 0.79 | 19 | empty |
| 5 | 75 | 0.32 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4014 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 4BMK · Serine Palmitoyltransferase K265A from S. paucimobilis with bound PLP- Myriocin Aldimine · 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 4BMK · PDBe 4BMK · UniProt Q93UV0
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