Research workbench
Crystal structure of stspl - apo form, after treatment with semicarbazide
Analyse Crystal structure of stspl - apo form, after treatment with semicarbazide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MBB
- Type
- protein
- Length
- 902 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sphingosine-1-phosphate lyase
- EC
- 4.1.2.27
- UniProt
- Q67PY4
- Ligands
- NA, PO4
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 451 | 46% helix, 14% strand | Q67PY4 |
| B | Putative sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 451 | 45% helix, 14% strand | Q67PY4 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.79 | 0.84 | 83 | PO4 |
| 2 | 137 | 0.79 | 0.96 | 37 | empty |
| 3 | 609 | 0.77 | 0.83 | 70 | PO4 |
| 4 | 50 | 0.71 | 0.99 | 18 | empty |
| 5 | 73 | 0.51 | 0.85 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 6502 Ų buried · 68 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 3MBB · Crystal structure of StSPL - apo form, after treatment with semicarbazide · 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 3MBB · PDBe 3MBB · UniProt Q67PY4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.