MolNFT v1 · #118448 · protein
Crystal structure of dual specific IMPASE/NADP phosphatase bound with D-inositol-1-phosphate
5F24 · Inositol monophosphatase: “Crystal structure of dual specific IMPASE/NADP phosphatase bound with D-inositol-1-phosphate”. X-ray diffraction, 3 ligands (IPD, CA, CL), 4 pockets (best druggability 0.67). MolNFT v1 #118448 on…
- PDB
- 5F24
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase
- EC
- 3.1.3.25
- UniProt
- A0A0D6HL44
- Ligands
- IPD, CA, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase (EC 3.1.3.25) | protein | 260 | 36% helix, 23% strand | A0A0D6HL44 |
| B | Inositol monophosphatase (EC 3.1.3.25) | protein | 255 | 35% helix, 25% strand | A0A0D6HL44 |
Ligands and binding sites
- IPD · D-myo-inositol-1-phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- P6G · Hexaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.67 | 0.81 | 37 | CA, IPD |
| 2 | 358 | 0.61 | 0.78 | 35 | CA, IPD |
| 3 | 267 | 0.52 | 0.75 | 39 | empty |
| 4 | 133 | 0.45 | 0.77 | 27 | GOL |
Interfaces
1 interface between chains.
- A–B · 1525 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5F24 · Crystal structure of dual specific IMPase/NADP phosphatase bound with… · 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 A0A0D6HL44
- Elsewhere: RCSB PDB 5F24 · PDBe 5F24 · UniProt A0A0D6HL44
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