Research workbench
Crystal structure of helicobacter pylori PPX/GPPA in complex with gsp
Analyse Crystal structure of helicobacter pylori PPX/GPPA in complex with gsp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PC3
- Type
- protein
- Length
- 966 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanosine pentaphosphate phosphohydrolase
- UniProt
- B5ZA44
- Ligands
- GSP, TS6, MG, K, CL, PO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Guanosine pentaphosphate phosphohydrolase | protein | 483 | 50% helix, 16% strand | B5ZA44 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains A, B
- TS6 · Monothiophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.84 | 0.84 | 94 | CL, GSP, MG |
| 2 | 1199 | 0.81 | 0.82 | 93 | GSP, MG, CL |
| 3 | 89 | 0.75 | 0.98 | 30 | PO4, MG, CL, TS6 |
| 4 | 85 | 0.74 | 0.97 | 29 | PO4, MG, TS6 |
| 5 | 174 | 0.45 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2377 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6PC3 · Crystal structure of Helicobacter pylori PPX/GppA in complex with GSP · 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 B5ZA44
- Elsewhere: RCSB PDB 6PC3 · PDBe 6PC3 · UniProt B5ZA44
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