Research workbench
Crystal structure of selenomonas ruminantium phytase complexed with persulfated phytate in the C2221 crystal form
Analyse Crystal structure of selenomonas ruminantium phytase complexed with persulfated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U25
- Type
- protein
- Length
- 933 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myo-inositol hexaphosphate phosphohydrolase
- EC
- 3.1.3.72
- UniProt
- Q7WUJ1
- Ligands
- IHS
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myo-inositol hexaphosphate phosphohydrolase (EC 3.1.3.72) | protein | 311 | 37% helix, 17% strand | Q7WUJ1 |
| B | Myo-inositol hexaphosphate phosphohydrolase (EC 3.1.3.72) | protein | 312 | 38% helix, 17% strand | Q7WUJ1 |
| C | Myo-inositol hexaphosphate phosphohydrolase (EC 3.1.3.72) | protein | 310 | 37% helix, 18% strand | Q7WUJ1 |
Ligands and binding sites
- IHS · D-myo-inositol-hexasulphate · ligand · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.78 | 0.80 | 114 | IHS |
| 2 | 796 | 0.71 | 0.77 | 92 | empty |
| 3 | 321 | 0.55 | 0.75 | 50 | empty |
| 4 | 123 | 0.52 | 0.82 | 24 | empty |
| 5 | 128 | 0.48 | 0.79 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–C · 477 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 457 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 1U25 · Crystal structure of Selenomonas ruminantium phytase complexed with persulfated phytate… · 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 1U25 · PDBe 1U25 · UniProt Q7WUJ1
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