Research workbench
Crystal structure of helicobacter pylori PPX/GPPA
Analyse Crystal structure of helicobacter pylori PPX/GPPA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PC0
- Type
- protein
- Length
- 962 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanosine pentaphosphate phosphohydrolase
- UniProt
- B5ZA44
- Ligands
- MLT, LMR, SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanosine pentaphosphate phosphohydrolase | protein | 478 | 48% helix, 17% strand | B5ZA44 |
| B | Guanosine pentaphosphate phosphohydrolase | protein | 484 | 48% helix, 17% strand | B5ZA44 |
Ligands and binding sites
- MLT · D-malate · ligand · 2 copies · chains A, B
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 22 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.86 | 0.87 | 111 | SO4, MLT, LMR |
| 2 | 1147 | 0.85 | 0.86 | 115 | SO4, MLT |
| 3 | 200 | 0.47 | 0.74 | 28 | empty |
| 4 | 193 | 0.46 | 0.75 | 25 | empty |
| 5 | 133 | 0.41 | 0.75 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 2331 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6PC0 · Crystal structure of Helicobacter pylori PPX/GppA · 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 6PC0 · PDBe 6PC0 · UniProt B5ZA44
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