MolNFT v1 · #179273 · protein
Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA
7K0I · Serine palmitoyltransferase 1: “Human serine palmitoyltransferase complex SPTLC1/SPLTC2/SSSPTA”. Electron microscopy, 2 ligands (POV, PLP), 18 pockets (best druggability 0.84). MolNFT v1 #179273 on GenesisL1: 3D structure, binding…
- PDB
- 7K0I
- Type
- protein
- Length
- 1,954 residues
- Chains
- 6
- 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
- POV, PLP
- Pockets
- 18 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 423 | 41% helix, 16% strand | O15269 |
| B, E | Serine palmitoyltransferase 2 (EC 2.3.1.50) | protein | 492 | 43% helix, 16% strand | O15270 |
| C, F | Serine palmitoyltransferase small subunit a | protein | 62 | 79% helix, 0% strand | Q969W0 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 4 copies · chains B, C, F, E
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.84 | 0.85 | 102 | PLP |
| 2 | 964 | 0.83 | 0.84 | 100 | PLP |
| 3 | 139 | 0.80 | 0.97 | 28 | empty |
| 4 | 142 | 0.80 | 0.97 | 26 | empty |
| 5 | 68 | 0.73 | 0.97 | 20 | empty |
Interfaces
7 interfaces between chains.
- D–E · 5041 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 5039 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 946 Ų buried · 5 hydrogen bonds · protein-protein
- F–E · 930 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 294 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7K0I · Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa · the same entry in another collection · chain E against E, 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
- 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 0.77
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 7K0I · PDBe 7K0I · UniProt O15269 · UniProt O15270 · UniProt Q969W0
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