Research workbench
Structure of the ptp-like myo-inositol phosphatase from desulfovibrio magneticus
Analyse Structure of the ptp-like myo-inositol phosphatase from desulfovibrio magneticus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K67
- Type
- protein
- Length
- 1,098 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myo-inositol phosphohydrolase
- UniProt
- C4XPJ9
- Ligands
- PO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myo-inositol phosphohydrolase | protein | 278 | 39% helix, 18% strand | C4XPJ9 |
| B | Myo-inositol phosphohydrolase | protein | 272 | 39% helix, 18% strand | C4XPJ9 |
| C | Myo-inositol phosphohydrolase | protein | 271 | 39% helix, 18% strand | C4XPJ9 |
| D | Myo-inositol phosphohydrolase | protein | 277 | 39% helix, 18% strand | C4XPJ9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- TAR · D(-)-tartaric acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.80 | 0.81 | 103 | empty |
| 2 | 1030 | 0.79 | 0.80 | 89 | empty |
| 3 | 133 | 0.54 | 0.82 | 23 | empty |
| 4 | 118 | 0.54 | 0.82 | 17 | empty |
| 5 | 247 | 0.52 | 0.76 | 38 | PO4, TAR |
Interfaces
6 interfaces between chains.
- B–C · 1200 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1168 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 798 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7K67 · Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus · 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 C4XPJ9
- Elsewhere: RCSB PDB 7K67 · PDBe 7K67 · UniProt C4XPJ9
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