Research workbench
S1P lyase bacterial surrogate bound to N-(1-(4-(3-hydroxyprop-1-yn-1- YL)PHENYL)-2-((4-methoxy-2,5-DIMETHYLBENZYL)AMINO)ETHYL)-5- methylisoxazole-3-carboxamide
Analyse S1P lyase bacterial surrogate bound to N-(1-(4-(3-hydroxyprop-1-yn-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EUD
- Type
- protein
- Length
- 903 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sphingosine-1-phosphate lyase
- UniProt
- Q67PY4
- Ligands
- 5S6, PO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sphingosine-1-phosphate lyase | protein | 454 | 46% helix, 13% strand | Q67PY4 |
| B | Putative sphingosine-1-phosphate lyase | protein | 449 | 46% helix, 14% strand | Q67PY4 |
Ligands and binding sites
- 5S6 · ~{N}-[(1~{S})-2-[(4-methoxy-2,5-dimethyl-phenyl)methylamino]-1-[4-(3-oxidanylprop-1-ynyl)phenyl]ethyl]-5-methyl-1,2-oxazole-3-carboxamide · ligand · 2 copies · chains A, B
- 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
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.82 | 0.85 | 68 | PO4, 5S6 |
| 2 | 124 | 0.78 | 0.96 | 37 | empty |
| 3 | 667 | 0.78 | 0.83 | 64 | 5S6, PO4 |
| 4 | 54 | 0.56 | 0.90 | 14 | empty |
| 5 | 164 | 0.48 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 6537 Ų buried · 72 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 5EUD · S1P Lyase Bacterial Surrogate bound to N-(1-(4-(3-hydroxyprop-1-yn-1-yl)phenyl)-2-((4-meth… · the same entry in another collection · chain B against B, 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 5EUD · PDBe 5EUD · UniProt Q67PY4
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