MolNFT v1 · #115817 · protein
Crystal structure of trypanosoma brucei vacuolar soluble pyrophosphatases in apo form
5CUY · Acidocalcisomal pyrophosphatase: “Crystal structure of trypanosoma brucei vacuolar soluble pyrophosphatases in apo form”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.85). MolNFT v1 #115817 on GenesisL1: 3D…
- PDB
- 5CUY
- Type
- protein
- Length
- 1,568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acidocalcisomal pyrophosphatase
- UniProt
- Q384W3
- Ligands
- MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acidocalcisomal pyrophosphatase | protein | 392 | 32% helix, 21% strand | Q384W3 |
| B | Acidocalcisomal pyrophosphatase | protein | 388 | 30% helix, 20% strand | Q384W3 |
| C | Acidocalcisomal pyrophosphatase | protein | 392 | 30% helix, 22% strand | Q384W3 |
| D | Acidocalcisomal pyrophosphatase | protein | 396 | 30% helix, 23% strand | Q384W3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.85 | 0.87 | 136 | CIT |
| 2 | 896 | 0.74 | 0.78 | 81 | MG |
| 3 | 892 | 0.74 | 0.78 | 74 | empty |
| 4 | 740 | 0.74 | 0.79 | 74 | MG |
| 5 | 742 | 0.71 | 0.77 | 66 | MG |
Interfaces
6 interfaces between chains.
- A–B · 4209 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 4176 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1907 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1874 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 960 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5CUY · Crystal structure of Trypanosoma brucei Vacuolar Soluble Pyrophosphatases in apo form · 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 Q384W3
- Elsewhere: RCSB PDB 5CUY · PDBe 5CUY · UniProt Q384W3
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