Research workbench
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 1
Analyse Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K0M
- Type
- protein
- Length
- 2,342 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens
- 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 0.88
Structure
electron microscopy · resolution 2.9 · 4 distinct chains · 47% helix, 13% 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 | 41% helix, 17% strand | O15270 |
| C, G | Serine palmitoyltransferase small subunit A | protein | 62 | 84% helix, 0% strand | Q969W0 |
| D, H | ORM1-like protein 3 | protein | 153 | 59% helix, 1% strand | Q8N138 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 14 copies · chains B, C, D, G, F, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.88 | 0.89 | 138 | PLP |
| 2 | 1156 | 0.88 | 0.89 | 141 | PLP |
| 3 | 193 | 0.82 | 0.97 | 31 | empty |
| 4 | 187 | 0.82 | 0.97 | 33 | empty |
| 5 | 866 | 0.80 | 0.82 | 51 | POV |
Interfaces
16 interfaces between chains.
- A–B · 4966 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 4958 Ų buried · 37 hydrogen bonds · protein-protein
- H–F · 1458 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1458 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1051 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7K0M · Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA/ORMDL3, class 1 · 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 0.89
- 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 7K0M · PDBe 7K0M · UniProt O15269 · UniProt O15270 · UniProt Q969W0 · UniProt Q8N138
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