Research workbench
Type II inorganic pyrophosphatase (ppase) from the psychrophilic bacterium shewanella sp. as-11, mn-activated 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
- 6LL7
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- UniProt
- L8AXY8
- Ligands
- MN, CA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Inorganic pyrophosphatase | protein | 306 | 42% helix, 21% strand | L8AXY8 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.78 | 0.81 | 104 | MN |
| 2 | 541 | 0.76 | 0.83 | 60 | empty |
| 3 | 539 | 0.76 | 0.83 | 59 | MN |
| 4 | 498 | 0.75 | 0.83 | 57 | empty |
| 5 | 232 | 0.52 | 0.76 | 35 | empty |
Interfaces
3 interfaces between chains.
- C–D · 936 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 922 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6LL7 · 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 6LL7 · PDBe 6LL7 · UniProt L8AXY8
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