Research workbench
Cryo-EM structure of the monomeric spt-ORMDL3 complex
Analyse Cryo-EM structure of the monomeric spt-ORMDL3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M4O
- Type
- protein
- Length
- 1,127 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
- PLP
- Pockets
- 12 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 36% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 420 | 32% helix, 11% strand | O15269 |
| T | Serine palmitoyltransferase 2 (EC 2.3.1.50) | protein | 491 | 31% helix, 16% strand | O15270 |
| A | ORM1-like protein 3 | protein | 139 | 43% helix, 1% strand | Q8N138 |
| E | Serine palmitoyltransferase small subunit a | protein | 49 | 78% helix, 0% strand | Q969W0 |
| B | Serine palmitoyltransferase 1 (EC 2.3.1.50) | protein | 28 | 54% helix, 0% strand | O15269 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.85 | 0.86 | 124 | PLP |
| 2 | 860 | 0.78 | 0.80 | 50 | empty |
| 3 | 107 | 0.78 | 0.97 | 27 | empty |
| 4 | 421 | 0.68 | 0.80 | 57 | empty |
| 5 | 57 | 0.65 | 0.94 | 20 | empty |
Interfaces
6 interfaces between chains.
- S–T · 5066 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 947 Ų buried · 3 hydrogen bonds · protein-protein
- T–E · 935 Ų buried · 6 hydrogen bonds · protein-protein
- T–A · 896 Ų buried · 10 hydrogen bonds · protein-protein
- S–A · 462 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6M4O · Cryo-EM structure of the monomeric SPT-ORMDL3 complex · the same entry in another collection · chain B against B, 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
- 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 0.96
- O15270 · AlphaFold monomer V2.0 prediction for serine palmitoyltransferase 2 (O15270) · a predicted model of the same protein · chain T against A, TM-score 0.96
- 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 0.86
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 6M4O · PDBe 6M4O · UniProt O15269 · UniProt O15270 · UniProt Q8N138 · UniProt Q969W0
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