MolNFT v1 · #179482 · protein
Structure of the ptp-like myo-inositol phosphatase from desulfovibrio magneticus in complex with myo-inositol hexakisphosphate
7K6W · Myo-inositol phosphohydrolase: “Structure of the ptp-like myo-inositol phosphatase from desulfovibrio magneticus in complex with myo-inositol…”. X-ray diffraction, 2 ligands (IHP, PO4), 19 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 7K6W
- Type
- protein
- Length
- 1,100 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myo-inositol phosphohydrolase
- UniProt
- C4XPJ9
- Ligands
- IHP, PO4
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myo-inositol phosphohydrolase | protein | 278 | 38% helix, 18% strand | C4XPJ9 |
| B | Myo-inositol phosphohydrolase | protein | 273 | 39% helix, 18% strand | C4XPJ9 |
| C | Myo-inositol phosphohydrolase | protein | 272 | 38% helix, 18% strand | C4XPJ9 |
| D | Myo-inositol phosphohydrolase | protein | 277 | 37% helix, 18% strand | C4XPJ9 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 13 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.79 | 0.81 | 78 | ACT |
| 2 | 828 | 0.79 | 0.82 | 77 | ACT |
| 3 | 155 | 0.55 | 0.81 | 22 | empty |
| 4 | 168 | 0.54 | 0.80 | 22 | empty |
| 5 | 234 | 0.50 | 0.76 | 38 | IHP, PO4, ACT |
Interfaces
6 interfaces between chains.
- B–C · 1255 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1251 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 751 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 747 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7K6W · Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus 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 C4XPJ9
- Elsewhere: RCSB PDB 7K6W · PDBe 7K6W · UniProt C4XPJ9
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