MolNFT v1 · #156450 · protein
Cryo-EM structure of the dimeric spt-ORMDL3 complex
6M4N · Serine palmitoyltransferase 1: “Cryo-EM structure of the dimeric spt-ORMDL3 complex”. Electron microscopy, 1 ligand (PLP), 20 pockets (best druggability 0.88). MolNFT v1 #156450 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6M4N
- Type
- protein
- Length
- 2,254 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine palmitoyltransferase 1; Serine palmitoyltransferase 2; ORM1-like protein 3; Serine…
- EC
- 2.3.1.50
- UniProt
- O15269, O15270, Q8N138, Q969W0
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 448 | 37% helix, 11% strand | O15269 |
| B, F | Serine palmitoyltransferase 2 (EC 2.3.1.50) | protein | 491 | 36% helix, 16% strand | O15270 |
| C, G | ORM1-like protein 3 | protein | 139 | 56% helix, 1% strand | Q8N138 |
| D, H | Serine palmitoyltransferase small subunit a | protein | 49 | 80% helix, 0% strand | Q969W0 |
Ligands and binding sites
- 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 | 922 | 0.88 | 0.89 | 126 | PLP |
| 2 | 827 | 0.86 | 0.89 | 117 | PLP |
| 3 | 132 | 0.79 | 0.97 | 29 | empty |
| 4 | 141 | 0.79 | 0.96 | 31 | empty |
| 5 | 829 | 0.78 | 0.81 | 50 | empty |
Interfaces
16 interfaces between chains.
- A–B · 4936 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 4926 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 910 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 897 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 888 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6M4N · Cryo-EM structure of the dimeric SPT-ORMDL3 complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q8N138 · AlphaFold monomer V2.0 prediction for ORM1-like protein 3 (Q8N138) · a predicted model of the same protein · chain C against A, TM-score 0.96
- O15270 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase 2 (O15270) · a predicted model of the same protein · chain B against A, TM-score 0.96
- O15269 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase 1 (O15269) · a predicted model of the same protein · chain A against A, TM-score 0.91
- Q969W0 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase small subunit a (Q969W0) · a predicted model of the same protein · chain D against A, TM-score 0.87
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 Q8N138
- Every structure of UniProt Q969W0
- Elsewhere: RCSB PDB 6M4N · PDBe 6M4N · UniProt O15269 · UniProt O15270 · UniProt Q8N138 · UniProt Q969W0
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