MolNFT v1 · #160151 · protein
Crystal structure of helicobacter pylori PPX/GPPA in complex with gnp
6PC2 · Guanosine pentaphosphate phosphohydrolase: “Crystal structure of helicobacter pylori PPX/GPPA in complex with gnp”. X-ray diffraction, 3 ligands (GNP, MG, PO4), 12 pockets (best druggability 0.83). MolNFT v1 #160151 on GenesisL1: 3D…
- PDB
- 6PC2
- Type
- protein
- Length
- 964 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanosine pentaphosphate phosphohydrolase
- UniProt
- B5ZA44
- Ligands
- GNP, MG, PO4
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Guanosine pentaphosphate phosphohydrolase | protein | 482 | 47% helix, 16% strand | B5ZA44 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.83 | 0.85 | 83 | MG, GNP |
| 2 | 1184 | 0.79 | 0.81 | 85 | MG, GNP |
| 3 | 96 | 0.75 | 0.97 | 35 | MG, PO4 |
| 4 | 81 | 0.71 | 0.96 | 31 | MG, PO4 |
| 5 | 121 | 0.58 | 0.84 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2527 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6PC2 · Crystal structure of Helicobacter pylori PPX/GppA in complex with GNP · 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 6PC2 · PDBe 6PC2 · UniProt B5ZA44
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