MolNFT v1 · #179275 · protein
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA, 3KS- bound
7K0K · Serine palmitoyltransferase 1: “Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA, 3KS- bound”. Electron microscopy, 2 ligands (PLP, VSD), 7 pockets (best druggability 0.82). MolNFT v1 #179275 on GenesisL1: 3D…
- PDB
- 7K0K
- Type
- protein
- Length
- 964 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine palmitoyltransferase 1; Serine palmitoyltransferase 2; Serine palmitoyltransferase…
- EC
- 2.3.1.50
- UniProt
- O15269, O15270, Q969W0
- Ligands
- PLP, VSD
- Pockets
- 7 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 423 | 43% helix, 16% strand | O15269 |
| B | Serine palmitoyltransferase 2 (EC 2.3.1.50) | protein | 492 | 43% helix, 17% strand | O15270 |
| C | Serine palmitoyltransferase small subunit a | protein | 49 | 90% helix, 0% strand | Q969W0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
- VSD · 3-Dehydrosphinganine · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.82 | 0.83 | 125 | PLP, VSD |
| 2 | 124 | 0.80 | 0.98 | 26 | empty |
| 3 | 201 | 0.52 | 0.77 | 31 | empty |
| 4 | 111 | 0.51 | 0.81 | 20 | empty |
| 5 | 75 | 0.43 | 0.80 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5110 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 940 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7K0K · Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa, 3KS-bound · the same entry in another collection · chain A against A, TM-score 1.00
- O15269 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase 1 (O15269) · a predicted model of the same protein · chain A against A, TM-score 0.97
- O15270 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase 2 (O15270) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q969W0 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase small subunit a (Q969W0) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 O15269
- Every structure of UniProt O15270
- Every structure of UniProt Q969W0
- Elsewhere: RCSB PDB 7K0K · PDBe 7K0K · UniProt O15269 · UniProt O15270 · UniProt Q969W0
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