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Crystal structure of a glycerophosphoryl diester phosphodiesterase (BDI_3922) from parabacteroides distasonis atcc 8503 at 1.55 a resolution
Analyse Crystal structure of a glycerophosphoryl diester phosphodiesterase (BDI_3922)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MZ2
- Type
- protein
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphoryl diester phosphodiesterase
- UniProt
- A6LIT8
- Ligands
- NA, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycerophosphoryl diester phosphodiesterase | protein | 285 | 38% helix, 19% strand | A6LIT8 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 9 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.79 | 0.81 | 109 | SO4 |
| 2 | 63 | 0.44 | 0.82 | 20 | PG4 |
| 3 | 76 | 0.43 | 0.80 | 25 | PG4 |
| 4 | 79 | 0.33 | 0.74 | 18 | SO4 |
| 5 | 73 | 0.33 | 0.75 | 17 | SO4 |
Interfaces
1 interface between chains.
- A–B · 430 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3MZ2 · Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from… · 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 A6LIT8
- Elsewhere: RCSB PDB 3MZ2 · PDBe 3MZ2 · UniProt A6LIT8
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