Research workbench
Crystal structure of exopolyphosphatase (ppx) from porphyromonas gingivalis in complex with sulfate and magnesium ions
Analyse Crystal structure of exopolyphosphatase (ppx) from porphyromonas gingivalis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EPQ
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exopolyphosphatase
- UniProt
- B2RHQ2
- Ligands
- MG, SO4
- Pockets
- 3 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative exopolyphosphatase | protein | 296 | 46% helix, 23% strand | B2RHQ2 |
| B | Putative exopolyphosphatase | protein | 292 | 48% helix, 24% strand | B2RHQ2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.89 | 0.91 | 121 | SO4, MG |
| 2 | 278 | 0.52 | 0.75 | 27 | empty |
| 3 | 248 | 0.52 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1975 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7EPQ · Crystal structure of exopolyphosphatase (PPX) from Porphyromonas gingivalis in complex… · 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 B2RHQ2
- Elsewhere: RCSB PDB 7EPQ · PDBe 7EPQ · UniProt B2RHQ2
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