Research workbench
Crystal structure of StSPL in complex with phosphoethanolamine
Analyse Crystal structure of StSPL in complex with phosphoethanolamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MAU
- Type
- protein
- Length
- 1,807 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Symbiobacterium thermophilum
- Molecule
- sphingosine-1-phosphate lyase
- EC
- 4.1.2.27
- UniProt
- Q67PY4
- Ligands
- EXT, PLR, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.9 · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 452 | 45% helix, 14% strand | Q67PY4 |
| B | sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 451 | 45% helix, 14% strand | Q67PY4 |
Ligands and binding sites
- EXT · {5-hydroxy-6-methyl-4-[(E)-{[2-(phosphonooxy)ethyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate · ligand · 3 copies · chains A, B, C, D
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.82 | 0.85 | 92 | EXT |
| 2 | 589 | 0.81 | 0.86 | 71 | EXT |
| 3 | 685 | 0.80 | 0.84 | 72 | EXT |
| 4 | 678 | 0.80 | 0.84 | 71 | PLR, PO4 |
| 5 | 149 | 0.80 | 0.96 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6619 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 6590 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 598 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3MAU · Crystal structure of stspl in complex with phosphoethanolamine · the same entry in another collection · chain A against A, TM-score 1.00
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 Q67PY4
- Elsewhere: RCSB PDB 3MAU · PDBe 3MAU · UniProt Q67PY4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.