Research workbench
Structure of burkholderia pseudomallei K96243 sphingosine-1-phosphate lyase BPSS2021
Analyse Structure of burkholderia pseudomallei K96243 sphingosine-1-phosphate lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K1R
- Type
- protein
- Length
- 879 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Burkholderia pseudomallei sphingosine-1-phosphate lyase BPSS2021
- UniProt
- Q63IP8
- Ligands
- PLP
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Burkholderia pseudomallei sphingosine-1-phosphate lyase BPSS2021 | protein | 439 | 46% helix, 15% strand | Q63IP8 |
| B | Burkholderia pseudomallei sphingosine-1-phosphate lyase BPSS2021 | protein | 440 | 47% helix, 15% strand | Q63IP8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.74 | 0.83 | 52 | PLP |
| 2 | 470 | 0.74 | 0.83 | 57 | PLP |
| 3 | 60 | 0.68 | 0.96 | 21 | empty |
| 4 | 187 | 0.53 | 0.79 | 31 | empty |
| 5 | 179 | 0.52 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 6577 Ų buried · 87 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5K1R · Structure of Burkholderia pseudomallei K96243 sphingosine-1-phosphate lyase Bpss2021 · 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 Q63IP8
- Elsewhere: RCSB PDB 5K1R · PDBe 5K1R · UniProt Q63IP8
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