Research workbench
Crystal structure of a phosphatase from a toxoplasma gondii
Analyse Crystal structure of a phosphatase from a toxoplasma gondii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D8K
- Type
- protein
- Length
- 1,395 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein phosphatase 2C
- UniProt
- A4GX63
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein phosphatase 2C | protein | 348 | 25% helix, 31% strand | A4GX63 |
| B | Protein phosphatase 2C | protein | 350 | 24% helix, 33% strand | A4GX63 |
| C | Protein phosphatase 2C | protein | 351 | 23% helix, 33% strand | A4GX63 |
| D | Protein phosphatase 2C | protein | 346 | 23% helix, 34% strand | A4GX63 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.78 | 0.81 | 76 | empty |
| 2 | 795 | 0.74 | 0.79 | 70 | empty |
| 3 | 887 | 0.73 | 0.77 | 86 | empty |
| 4 | 567 | 0.70 | 0.79 | 62 | empty |
| 5 | 102 | 0.63 | 0.88 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–C · 762 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 757 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 569 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 502 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 3D8K · Crystal structure of a phosphatase from a toxoplasma gondii · 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 A4GX63
- Elsewhere: RCSB PDB 3D8K · PDBe 3D8K · UniProt A4GX63
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