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Crystal structure of putative glycerophosphoryl diester phosphodiesterase (YP_165505.1) from silicibacter pomeroyi dss-3 at 1.60 a resolution
Analyse Crystal structure of putative glycerophosphoryl diester phosphodiesterase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L12
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycerophosphoryl diester phosphodiesterase
- UniProt
- Q5LX22
- Ligands
- UNL, MG, CL
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glycerophosphoryl diester phosphodiesterase | protein | 297 | 38% helix, 19% strand | Q5LX22 |
| B | Putative glycerophosphoryl diester phosphodiesterase | protein | 295 | 37% helix, 19% strand | Q5LX22 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, 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 | 82 | 0.61 | 0.89 | 27 | empty |
| 2 | 92 | 0.41 | 0.78 | 22 | CL, UNL |
| 3 | 58 | 0.40 | 0.81 | 16 | empty |
| 4 | 83 | 0.40 | 0.78 | 26 | UNL |
| 5 | 77 | 0.37 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1013 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3L12 · Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (YP_165505.1)… · 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 Q5LX22
- Elsewhere: RCSB PDB 3L12 · PDBe 3L12 · UniProt Q5LX22
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