MolNFT v1 · #175430 · protein
Cryo-EM structure of the substrate-bound spt-ORMDL3 complex
7CQK · Serine palmitoyltransferase 1: “Cryo-EM structure of the substrate-bound spt-ORMDL3 complex”. Electron microscopy, 2 ligands (PLS, GE0), 17 pockets (best druggability 0.88). MolNFT v1 #175430 on GenesisL1: 3D structure, binding…
- PDB
- 7CQK
- Type
- protein
- Length
- 1,116 residues
- Chains
- 5
- 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
- PLS, GE0
- Pockets
- 17 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 37% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 421 | 31% helix, 15% strand | O15269 |
| T | Serine palmitoyltransferase 2 (EC 2.3.1.50) | protein | 497 | 34% helix, 15% strand | O15270 |
| A | ORM1-like protein 3 | protein | 130 | 54% helix, 2% strand | Q8N138 |
| E | Serine palmitoyltransferase small subunit a | protein | 46 | 67% helix, 0% strand | Q969W0 |
| C | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 22 | 73% helix, 0% strand | O15269 |
Ligands and binding sites
- PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · chains S, T
- GE0 · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-(2-oxidanylideneheptadecylsulfanyl) ethylamino]propyl]amino]butyl] hydrogen phosphate · ligand · chains S, T, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.88 | 0.89 | 129 | PLS |
| 2 | 201 | 0.82 | 0.96 | 38 | empty |
| 3 | 1111 | 0.73 | 0.75 | 53 | empty |
| 4 | 63 | 0.57 | 0.90 | 17 | empty |
| 5 | 107 | 0.55 | 0.84 | 23 | empty |
Interfaces
6 interfaces between chains.
- S–T · 5025 Ų buried · 36 hydrogen bonds · protein-protein
- T–E · 895 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 647 Ų buried · 1 hydrogen bond · protein-protein
- T–A · 640 Ų buried · 4 hydrogen bonds · protein-protein
- S–A · 280 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7CQK · Cryo-EM structure of the substrate-bound SPT-ORMDL3 complex · the same entry in another collection · chain C against C, TM-score 1.00
- O15269 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase 1 (O15269) · a predicted model of the same protein · chain S 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 T against A, TM-score 0.95
- Q8N138 · AlphaFold monomer V2.0 prediction for ORM1-like protein 3 (Q8N138) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q969W0 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase small subunit a (Q969W0) · a predicted model of the same protein · chain E against A, TM-score 0.84
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 7CQK · PDBe 7CQK · UniProt O15269 · UniProt O15270 · UniProt Q8N138 · UniProt Q969W0
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