Research workbench
Crystal structure of inorganic pyrophosphatase from helicobacter pylori
Analyse Crystal structure of inorganic pyrophosphatase from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YGZ
- Type
- protein
- Length
- 1,032 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P56153
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 172 | 19% helix, 35% strand | P56153 |
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.74 | 0.78 | 59 | empty |
| 2 | 949 | 0.74 | 0.77 | 80 | empty |
| 3 | 196 | 0.59 | 0.81 | 31 | empty |
| 4 | 215 | 0.58 | 0.80 | 32 | empty |
| 5 | 209 | 0.57 | 0.80 | 31 | empty |
Interfaces
9 interfaces between chains.
- E–F · 643 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 619 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 606 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 318 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 298 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1YGZ · Crystal Structure of Inorganic Pyrophosphatase from Helicobacter pylori · the same entry in another collection · chain C against C, TM-score 1.00
- P56153 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (P56153) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P56153
- Elsewhere: RCSB PDB 1YGZ · PDBe 1YGZ · UniProt P56153
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