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Structure of the ptp-like myo-inositol phosphatase from selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate
Analyse Structure of the ptp-like myo-inositol phosphatase from selenomonas ruminantium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WU2
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myo-inositol phosphohydrolase
- EC
- 3.1.3.8
- UniProt
- Q7WUJ1
- Ligands
- I3P, PO4, CL
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Myo-inositol phosphohydrolase (EC 3.1.3.8) | protein | 313 | 38% helix, 18% strand | Q7WUJ1 |
Ligands and binding sites
- I3P · D-myo-inositol-1,4,5-triphosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.62 | 0.77 | 32 | empty |
| 2 | 381 | 0.58 | 0.75 | 53 | I3P, PO4, GOL |
| 3 | 253 | 0.55 | 0.77 | 40 | I3P, PO4, GOL |
| 4 | 168 | 0.54 | 0.80 | 32 | empty |
| 5 | 114 | 0.46 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 679 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4WU2 · Structure of the PTP-like myo-inositol phosphatase from Selenomonas ruminantium in… · 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 Q7WUJ1
- Elsewhere: RCSB PDB 4WU2 · PDBe 4WU2 · UniProt Q7WUJ1
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