Research workbench
Recombinant inorganic pyrophosphatase from T brucei brucei
Analyse Recombinant inorganic pyrophosphatase from T brucei brucei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C5V
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acidocalcisomal pyrophosphatase
- UniProt
- Q384W5
- Ligands
- 2PN, MG, CL, BR
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acidocalcisomal pyrophosphatase | protein | 342 | 32% helix, 24% strand | Q384W5 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- BR · Bromide ion · ion · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.54 | 0.81 | 31 | 2PN, MG, CL |
| 2 | 164 | 0.50 | 0.78 | 34 | 2PN, MG, CL |
| 3 | 137 | 0.42 | 0.75 | 23 | empty |
| 4 | 142 | 0.42 | 0.75 | 26 | empty |
| 5 | 79 | 0.39 | 0.78 | 17 | CL |
Interfaces
1 interface between chains.
- A–B · 850 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5C5V · Recombinant Inorganic Pyrophosphatase from T brucei brucei · 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 Q384W5
- Elsewhere: RCSB PDB 5C5V · PDBe 5C5V · UniProt Q384W5
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