MolNFT v1 · #160150 · protein
Crystal structure of helicobacter pylori PPX/GPPA (E143A) in complex with ppgpp
6PC1 · Guanosine pentaphosphate phosphohydrolase: “Crystal structure of helicobacter pylori PPX/GPPA (E143A) in complex with ppgpp”. X-ray diffraction, 4 ligands (LMR, G4P, MG), 20 pockets (best druggability 0.85). MolNFT v1 #160150 on…
- PDB
- 6PC1
- Type
- protein
- Length
- 1,915 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanosine pentaphosphate phosphohydrolase
- UniProt
- B5ZA44
- Ligands
- LMR, G4P, MG, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Guanosine pentaphosphate phosphohydrolase | protein | 482 | 49% helix, 16% strand | B5ZA44 |
| B | Guanosine pentaphosphate phosphohydrolase | protein | 483 | 48% helix, 16% strand | B5ZA44 |
| D | Guanosine pentaphosphate phosphohydrolase | protein | 468 | 46% helix, 16% strand | B5ZA44 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 5 copies · chains A, B, C, D
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.85 | 0.86 | 111 | MG, G4P, PO4, LMR |
| 2 | 1078 | 0.84 | 0.85 | 92 | G4P |
| 3 | 919 | 0.83 | 0.85 | 83 | G4P, MG |
| 4 | 769 | 0.80 | 0.84 | 72 | G4P |
| 5 | 193 | 0.80 | 0.95 | 35 | PO4, LMR |
Interfaces
5 interfaces between chains.
- C–D · 2267 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2241 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 517 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PC1 · Crystal structure of Helicobacter pylori PPX/GppA (E143A) in complex with ppGpp · 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 6PC1 · PDBe 6PC1 · UniProt B5ZA44
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