Research workbench
Crystal structure of StSPL (asymmetric form)
Analyse Crystal structure of StSPL (asymmetric form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MAF
- Type
- protein
- Length
- 836 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.971
- Source
- Symbiobacterium thermophilum
- Molecule
- sphingosine-1-phosphate lyase
- EC
- 4.1.2.27
- UniProt
- Q67PY4
- Ligands
- CL, PO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.971 · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 441 | 45% helix, 14% strand | Q67PY4 |
| B | sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 395 | 43% helix, 15% strand | Q67PY4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.77 | 0.96 | 33 | empty |
| 2 | 525 | 0.75 | 0.83 | 63 | CL |
| 3 | 418 | 0.73 | 0.83 | 61 | PO4 |
| 4 | 268 | 0.65 | 0.82 | 39 | empty |
| 5 | 155 | 0.49 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 5500 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 3MAF · Crystal structure of stspl (asymmetric form) · 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 3MAF · PDBe 3MAF · UniProt Q67PY4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.