MolNFT v1 · #71366 · protein
Crystal structure of SCDPL1
3MC6 · Sphingosine-1-phosphate lyase: “Crystal structure of SCDPL1”. X-ray diffraction, 1 ligand (PO4), 14 pockets (best druggability 0.50). MolNFT v1 #71366 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MC6
- Type
- protein
- Length
- 850 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
- Q05567
- Ligands
- PO4
- Pockets
- 14 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 426 | 38% helix, 13% strand | Q05567 |
| C | Sphingosine-1-phosphate lyase (EC 4.1.2.27) | protein | 424 | 38% helix, 13% strand | Q05567 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.50 | 0.76 | 29 | empty |
| 2 | 229 | 0.50 | 0.75 | 24 | empty |
| 3 | 173 | 0.49 | 0.77 | 28 | empty |
| 4 | 152 | 0.46 | 0.76 | 24 | empty |
| 5 | 146 | 0.44 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 772 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
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 Q05567
- Elsewhere: RCSB PDB 3MC6 · PDBe 3MC6 · UniProt Q05567
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