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Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus anthraci
Analyse Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R7O
- Type
- protein
- Length
- 1,934 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.534
- Source
- Bacillus anthracis str. Ames
- Molecule
- Glycerophosphoryl diester phosphodiesterase, putative
- UniProt
- Q81YI6
- Ligands
- MG, SO4
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.534 · 5 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glycerophosphoryl diester phosphodiesterase, putative | protein | 279 | 33% helix, 19% strand | Q81YI6 |
| C | Glycerophosphoryl diester phosphodiesterase, putative | protein | 280 | 33% helix, 19% strand | Q81YI6 |
| E | Glycerophosphoryl diester phosphodiesterase, putative | protein | 275 | 34% helix, 19% strand | Q81YI6 |
| F | Glycerophosphoryl diester phosphodiesterase, putative | protein | 270 | 33% helix, 20% strand | Q81YI6 |
| G | Glycerophosphoryl diester phosphodiesterase, putative | protein | 272 | 34% helix, 20% strand | Q81YI6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, F, B, E, D, G
- GOL · Glycerol · additive · 4 copies · chains A, B, D, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, E
- EDO · 1,2-ethanediol · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.79 | 0.81 | 74 | EDO, SO4 |
| 2 | 779 | 0.72 | 0.78 | 95 | MG, GOL |
| 3 | 335 | 0.67 | 0.82 | 57 | MG, GOL, PEG |
| 4 | 462 | 0.60 | 0.75 | 47 | SO4 |
| 5 | 339 | 0.59 | 0.77 | 45 | MG, GOL |
Interfaces
12 interfaces between chains.
- A–E · 557 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 475 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 401 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 368 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4R7O · Crystal structure of putative glycerophosphoryl diester phosphodiesterasefrom bacillus… · 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 Q81YI6
- Elsewhere: RCSB PDB 4R7O · PDBe 4R7O · UniProt Q81YI6
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