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Crystal structure of putative glycerophosphoryl diester phosphodiesterase (NP_812074.1) from bacteroides thetaiotaomicron vpi-5482 at 1.35 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
- 3I10
- Type
- protein
- Length
- 278 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycerophosphoryl diester phosphodiesterase
- UniProt
- Q8A2Z3
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glycerophosphoryl diester phosphodiesterase | protein | 278 | 40% helix, 21% strand | Q8A2Z3 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 18 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.40 | 0.81 | 14 | EDO |
| 2 | 81 | 0.38 | 0.77 | 18 | PEG |
| 3 | 54 | 0.34 | 0.79 | 12 | EDO |
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 3I10 · Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (NP_812074.1)… · 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 Q8A2Z3
- Elsewhere: RCSB PDB 3I10 · PDBe 3I10 · UniProt Q8A2Z3
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