Research workbench
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA/ORMDL3, myriocin-bound
Analyse Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA/ORMDL3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K0Q
- Type
- protein
- Length
- 1,107 residues
- Chains
- 4
- 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
- PLP, VRP
- Pockets
- 12 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 48% helix, 13% 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, 16% strand | O15270 |
| C | Serine palmitoyltransferase small subunit a | protein | 49 | 82% helix, 0% strand | Q969W0 |
| D | ORM1-like protein 3 | protein | 143 | 69% helix, 1% strand | Q8N138 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.89 | 0.90 | 128 | PLP, VRP |
| 2 | 167 | 0.81 | 0.97 | 30 | empty |
| 3 | 975 | 0.79 | 0.80 | 50 | empty |
| 4 | 233 | 0.56 | 0.78 | 32 | empty |
| 5 | 194 | 0.55 | 0.79 | 37 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5107 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 946 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 876 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 548 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 192 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7K0Q · Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, myriocin-bound · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.97
- 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
- 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
- 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 0.90
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 7K0Q · PDBe 7K0Q · UniProt O15269 · UniProt O15270 · UniProt Q969W0 · UniProt Q8N138
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