MolNFT v1 · #103866 · protein
Crystal structure of staphylococcal impase-I complex with 3MG2+ and phosphate
4PTK · Inositol monophosphatase family protein: “Crystal structure of staphylococcal impase-I complex with 3MG2+ and phosphate”. X-ray diffraction, 2 ligands (MG, PO4), 5 pockets (best druggability 0.72). MolNFT v1 #103866 on GenesisL1: 3D…
- PDB
- 4PTK
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase family protein
- UniProt
- Q6G709
- Ligands
- MG, PO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase family protein | protein | 262 | 35% helix, 26% strand | Q6G709 |
| B | Inositol monophosphatase family protein | protein | 261 | 35% helix, 26% strand | Q6G709 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.72 | 0.81 | 39 | MG, PO4, GOL |
| 2 | 534 | 0.71 | 0.80 | 37 | PO4, MG, GOL |
| 3 | 57 | 0.69 | 0.97 | 24 | empty |
| 4 | 207 | 0.44 | 0.73 | 32 | empty |
| 5 | 173 | 0.41 | 0.73 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1555 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4PTK · Crystal structure of Staphylococcal IMPase-I complex with 3Mg2+ and Phosphate · 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 Q6G709
- Elsewhere: RCSB PDB 4PTK · PDBe 4PTK · UniProt Q6G709
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