Research workbench
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA/ORMDL3, class 2
Analyse Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA/ORMDL3, class 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K0N
- Type
- protein
- Length
- 2,340 residues
- Chains
- 8
- 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, Q8N138
- Ligands
- POV, PLP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 464 | 44% helix, 14% strand | O15269 |
| B, F | Serine palmitoyltransferase 2 (EC 2.3.1.50) | protein | 491 | 43% helix, 15% strand | O15270 |
| C, G | Serine palmitoyltransferase small subunit a | protein | 62 | 77% helix, 0% strand | Q969W0 |
| D, H | ORM1-like protein 3 | protein | 153 | 57% helix, 2% strand | Q8N138 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 16 copies · chains B, C, D, H, F, G
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.89 | 0.91 | 145 | PLP |
| 2 | 1190 | 0.88 | 0.89 | 148 | PLP |
| 3 | 204 | 0.82 | 0.96 | 32 | empty |
| 4 | 207 | 0.82 | 0.96 | 37 | empty |
| 5 | 773 | 0.79 | 0.82 | 44 | POV |
Interfaces
16 interfaces between chains.
- E–F · 4909 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 4908 Ų buried · 39 hydrogen bonds · protein-protein
- H–F · 1397 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1393 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1020 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7K0N · Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 2 · the same entry in another collection · chain F against F, TM-score 1.00
- 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
- Q8N138 · AlphaFold monomer V2.0 prediction for ORM1-like protein 3 (Q8N138) · a predicted model of the same protein · chain D against A, TM-score 0.93
- O15269 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase 1 (O15269) · a predicted model of the same protein · chain A against A, TM-score 0.89
- 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 0.76
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
- Every structure of UniProt Q8N138
- Elsewhere: RCSB PDB 7K0N · PDBe 7K0N · UniProt O15269 · UniProt O15270 · UniProt Q969W0 · UniProt Q8N138
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