Research workbench
Type II inorganic pyrophosphatase (ppase) from the psychrophilic bacterium shewanella sp. as-11, mg-pnp form
Analyse Type II inorganic pyrophosphatase (ppase) from the psychrophilic bacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LL8
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- UniProt
- L8AXY8
- Ligands
- 2PN, MG, CA, F
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inorganic pyrophosphatase | protein | 306 | 42% helix, 22% strand | L8AXY8 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 10 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
- F · Fluoride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.79 | 0.96 | 40 | MG, 2PN |
| 2 | 155 | 0.78 | 0.95 | 41 | MG, 2PN |
| 3 | 178 | 0.46 | 0.75 | 28 | empty |
| 4 | 98 | 0.40 | 0.77 | 18 | empty |
| 5 | 55 | 0.35 | 0.78 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1184 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6LL8 · Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp.… · 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 L8AXY8
- Elsewhere: RCSB PDB 6LL8 · PDBe 6LL8 · UniProt L8AXY8
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