MolNFT v1 · #126138 · protein
Crystal structure of NUDT4A- diphosphoinositol polyphosphate phosphohydrolase 2
5LTU: “Crystal structure of NUDT4A- diphosphoinositol polyphosphate phosphohydrolase 2”. X-ray diffraction, 1 pocket (best druggability 0.38). MolNFT v1 #126138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LTU
- Type
- protein
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphosphoinositol polyphosphate phosphohydrolase 2
- EC
- 3.6.1.52, 3.6.1.-
- UniProt
- Q9NZJ9
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphosphoinositol polyphosphate phosphohydrolase 2 (EC 3.6.1.52, 3.6.1.-) | protein | 127 | 28% helix, 42% strand | Q9NZJ9 |
| B | Diphosphoinositol polyphosphate phosphohydrolase 2 (EC 3.6.1.52, 3.6.1.-) | protein | 130 | 25% helix, 41% strand | Q9NZJ9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.38 | 0.79 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 272 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LTU · Crystal Structure of NUDT4A- Diphosphoinositol polyphosphate phosphohydrolase 2 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NZJ9 · AlphaFold monomer V2.0 prediction for diphosphoinositol polyphosphate phosphohydrolase 2… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9NZJ9
- Elsewhere: RCSB PDB 5LTU · PDBe 5LTU · UniProt Q9NZJ9
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