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Crystal structure of glycerophosphoryl diester phosphodiesterase from staphylococcus aureus
Analyse Crystal structure of glycerophosphoryl diester phosphodiesterase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OOG
- Type
- protein
- Length
- 1,603 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphoryl diester phosphodiesterase
- EC
- 3.1.4.46
- UniProt
- Q7A6H7
- Ligands
- ZN, SO4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Glycerophosphoryl diester phosphodiesterase (EC 3.1.4.46) | protein | 267 | 39% helix, 16% strand | Q7A6H7 |
| D | Glycerophosphoryl diester phosphodiesterase (EC 3.1.4.46) | protein | 268 | 37% helix, 16% strand | Q7A6H7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 39 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.74 | 0.77 | 90 | GOL |
| 2 | 628 | 0.73 | 0.80 | 51 | GOL |
| 3 | 598 | 0.72 | 0.80 | 45 | empty |
| 4 | 1122 | 0.71 | 0.75 | 104 | SO4 |
| 5 | 236 | 0.49 | 0.74 | 26 | GOL |
Interfaces
7 interfaces between chains.
- A–C · 584 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 458 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 454 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 257 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2OOG · Crystal structure of glycerophosphoryl diester phosphodiesterase from Staphylococcus… · 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 Q7A6H7
- Elsewhere: RCSB PDB 2OOG · PDBe 2OOG · UniProt Q7A6H7
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