MolNFT v1 · #179279 · protein
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA/ORMDL3, class 3
7K0O · Serine palmitoyltransferase 1: “Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA/ORMDL3, class 3”. Electron microscopy, 2 ligands (POV, PLP), 20 pockets (best druggability 0.87). MolNFT v1 #179279 on GenesisL1: 3D…
- PDB
- 7K0O
- Type
- protein
- Length
- 2,342 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 0.87
Structure
electron microscopy · 4 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 464 | 45% helix, 14% strand | O15269 |
| B, F | Serine palmitoyltransferase 2 (EC 2.3.1.50) | protein | 492 | 43% helix, 15% strand | O15270 |
| C, G | Serine palmitoyltransferase small subunit a | protein | 62 | 79% helix, 0% strand | Q969W0 |
| D, H | ORM1-like protein 3 | protein | 153 | 60% helix, 1% strand | Q8N138 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 12 copies · chains B, C, D, E, G, F, A, H
- 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.87 | 0.88 | 146 | PLP |
| 2 | 1166 | 0.86 | 0.87 | 151 | PLP |
| 3 | 165 | 0.81 | 0.96 | 28 | empty |
| 4 | 161 | 0.80 | 0.96 | 28 | empty |
| 5 | 901 | 0.79 | 0.81 | 48 | POV |
Interfaces
15 interfaces between chains.
- A–B · 5035 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 5019 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 1427 Ų buried · 15 hydrogen bonds · protein-protein
- H–F · 1427 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 1065 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7K0O · Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 3 · the same entry in another collection · chain H against H, 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 0.94
- O15269 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase 1 (O15269) · a predicted model of the same protein · chain A against A, TM-score 0.90
- 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 7K0O · PDBe 7K0O · UniProt O15269 · UniProt O15270 · UniProt Q969W0 · UniProt Q8N138
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