Research workbench
Crystal structure of stspl (symmetric form)
Analyse Crystal structure of stspl (symmetric form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MAD
- Type
- protein
- Length
- 902 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingosine-1-phosphate lyase
- EC
- 4.1.2.27
- UniProt
- Q67PY4
- Ligands
- PO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 451 | 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
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.81 | 0.97 | 42 | empty |
| 2 | 583 | 0.77 | 0.83 | 64 | PO4 |
| 3 | 449 | 0.74 | 0.83 | 49 | PO4 |
| 4 | 51 | 0.71 | 0.99 | 18 | empty |
| 5 | 53 | 0.65 | 0.94 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 6475 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 3MAD · Crystal structure of StSPL (symmetric 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 3MAD · PDBe 3MAD · UniProt Q67PY4
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