MolNFT v1 · #108495 · protein
Crystal structure of LPSPL/LPP2128, legionella pneumophila sphingosine-1 phosphate lyase
4W8I · Probable sphingosine-1-phosphate lyase: “Crystal structure of LPSPL/LPP2128, legionella pneumophila sphingosine-1 phosphate lyase”. X-ray diffraction, 12 pockets (best druggability 0.72). MolNFT v1 #108495 on GenesisL1: 3D…
- PDB
- 4W8I
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable sphingosine-1-phosphate lyase
- EC
- 4.1.2.27
- UniProt
- Q5X3A8
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 363 | 42% helix, 15% strand | Q5X3A8 |
| B | Probable sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 354 | 39% helix, 15% strand | Q5X3A8 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.72 | 0.78 | 84 | empty |
| 2 | 195 | 0.53 | 0.78 | 27 | empty |
| 3 | 196 | 0.52 | 0.77 | 21 | empty |
| 4 | 154 | 0.49 | 0.78 | 29 | empty |
| 5 | 82 | 0.43 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3138 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4W8I · Crystal structure of LpSPL/Lpp2128, Legionella pneumophila sphingosine-1 phosphate lyase · the same entry in another collection · chain A against A, TM-score 1.00
- Q5X3A8 · AlphaFold monomer V2.0 prediction for probable sphingosine-1-phosphate lyase (Q5X3A8) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q5X3A8
- Elsewhere: RCSB PDB 4W8I · PDBe 4W8I · UniProt Q5X3A8
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