Research workbench
Crystal structure of IMPASE/NADP phosphatase complexed with MG2+ and phosphate
Analyse Crystal structure of IMPASE/NADP phosphatase complexed with MG2+ and phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G61
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase family protein
- EC
- 3.1.3.25
- UniProt
- Q6G709
- Ligands
- DTO, MG, PO4, CL
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase family protein (EC 3.1.3.25) | protein | 264 | 36% helix, 25% strand | Q6G709 |
| B | Inositol monophosphatase family protein (EC 3.1.3.25) | protein | 261 | 36% helix, 26% strand | Q6G709 |
Ligands and binding sites
- DTO · 1-hydroxysulfanyl-4-mercapto-butane-2,3-diol · ligand · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains B
- PG4 · Tetraethylene glycol · additive · 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 | 531 | 0.74 | 0.82 | 42 | PO4, MG, GOL |
| 2 | 513 | 0.71 | 0.81 | 35 | MG, PO4, GOL |
| 3 | 92 | 0.71 | 0.94 | 30 | CL, DTO |
| 4 | 144 | 0.39 | 0.73 | 28 | PG4 |
| 5 | 120 | 0.36 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1610 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4G61 · Crystal structure of IMPase/NADP phosphatase complexed with Mg2+ 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 4G61 · PDBe 4G61 · UniProt Q6G709
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