MolNFT v1 · #179484 · protein
Structure of the ptp-like myo-inositol phosphatase from desulfovibrio magneticus (high salt)
7K6Y · Myo-inositol phosphohydrolase: “Structure of the ptp-like myo-inositol phosphatase from desulfovibrio magneticus (high salt)”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.79). MolNFT v1 #179484 on GenesisL1: 3D…
- PDB
- 7K6Y
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myo-inositol phosphohydrolase
- UniProt
- C4XPJ9
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myo-inositol phosphohydrolase | protein | 278 | 40% helix, 19% strand | C4XPJ9 |
| B | Myo-inositol phosphohydrolase | protein | 276 | 40% helix, 19% strand | C4XPJ9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
- ACT · Acetate ion · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.79 | 0.81 | 92 | SO4 |
| 2 | 157 | 0.48 | 0.78 | 27 | SO4 |
| 3 | 191 | 0.48 | 0.76 | 28 | SO4 |
| 4 | 113 | 0.47 | 0.79 | 15 | empty |
| 5 | 124 | 0.47 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1170 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7K6Y · Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus (high… · 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 7K6Y · PDBe 7K6Y · UniProt C4XPJ9
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