MolNFT v1 · #113179 · protein
Crystal structure of INPP5B in complex with benzene 1,2,4,5- tetrakisphosphate
5A7J · Type II inositol 1,4,5-trisphosphate 5-phosphatase: “Crystal structure of INPP5B in complex with benzene 1,2,4,5- tetrakisphosphate”. X-ray diffraction, 2 ligands (K2Y, SO4), 5 pockets (best druggability 0.50). MolNFT v1 #113179 on…
- PDB
- 5A7J
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II inositol 1,4,5-trisphosphate 5-phosphatase
- EC
- 3.1.3.36
- UniProt
- P32019
- Ligands
- K2Y, SO4
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type II inositol 1,4,5-trisphosphate 5-phosphatase (EC 3.1.3.36) | protein | 309 | 21% helix, 36% strand | P32019 |
Ligands and binding sites
- K2Y · (2,4,5-triphosphonooxyphenyl) dihydrogen phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.50 | 0.76 | 27 | empty |
| 2 | 122 | 0.44 | 0.77 | 28 | empty |
| 3 | 146 | 0.42 | 0.75 | 32 | empty |
| 4 | 62 | 0.28 | 0.73 | 11 | empty |
| 5 | 57 | 0.27 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 96 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A7J · Crystal structure of INPP5B in complex with benzene 1,2,4,5- tetrakisphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P32019 · AlphaFold monomer V2.0 prediction for type II inositol 1,4,5-trisphosphate 5-phosphatase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P32019
- Elsewhere: RCSB PDB 5A7J · PDBe 5A7J · UniProt P32019
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