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The crystal structure of the glycerophosphodiester phosphodiesterase from shigella flexneri 2A
Analyse The crystal structure of the glycerophosphodiester phosphodiesterase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OTD
- Type
- protein
- Length
- 980 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphodiester phosphodiesterase
- EC
- 3.1.4.1
- UniProt
- Q83PU8
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycerophosphodiester phosphodiesterase (EC 3.1.4.1) | protein | 245 | 34% helix, 19% strand | Q83PU8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.64 | 0.77 | 44 | empty |
| 2 | 189 | 0.55 | 0.79 | 28 | empty |
| 3 | 183 | 0.53 | 0.79 | 26 | empty |
| 4 | 166 | 0.53 | 0.79 | 23 | empty |
| 5 | 169 | 0.49 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 592 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 538 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 479 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2OTD · The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella… · 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 Q83PU8
- Elsewhere: RCSB PDB 2OTD · PDBe 2OTD · UniProt Q83PU8
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