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Crystal structure of sphingosine kinase 1
Analyse Crystal structure of sphingosine kinase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZB
- Type
- protein
- Length
- 1,043 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingosine kinase 1
- EC
- 2.7.1.91
- UniProt
- Q9NYA1
- Ligands
- SQS, SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 360 | 32% helix, 31% strand | Q9NYA1 |
| B | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 339 | 31% helix, 32% strand | Q9NYA1 |
| C | Sphingosine kinase 1 (EC 2.7.1.91) | protein | 344 | 32% helix, 31% strand | Q9NYA1 |
Ligands and binding sites
- SQS · (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.86 | 0.90 | 73 | SO4 |
| 2 | 678 | 0.86 | 0.90 | 89 | SQS, SO4, EDO |
| 3 | 360 | 0.82 | 0.91 | 62 | SQS, SO4 |
| 4 | 471 | 0.77 | 0.84 | 30 | empty |
| 5 | 414 | 0.67 | 0.79 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–C · 525 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 471 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 336 Ų buried · 0 hydrogen bonds · protein-protein
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 Q9NYA1
- Elsewhere: RCSB PDB 3VZB · PDBe 3VZB · UniProt Q9NYA1
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