MolNFT v1 · #11516 · protein
Crystal structure of an enzyme displaying both inositol-polyphosphate 1-phosphatase and 3'-phosphoadenosine-5'-phosphate phosphatase activities
1JP4 · 3'(2'),5'-bisphosphate nucleotidase: “Crystal structure of an enzyme displaying both inositol-polyphosphate 1-phosphatase and…”. X-ray diffraction, 3 ligands (AMP, MG, PO4), 2 pockets (best druggability 0.71). MolNFT v1 #11516 on…
- PDB
- 1JP4
- Type
- protein
- Length
- 302 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3'(2'),5'-bisphosphate nucleotidase
- EC
- 3.1.3.7, 3.1.3.57
- UniProt
- Q9Z1N4
- Ligands
- AMP, MG, PO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3'(2'),5'-bisphosphate nucleotidase (EC 3.1.3.7, 3.1.3.57) | protein | 302 | 35% helix, 23% strand | Q9Z1N4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.71 | 0.88 | 36 | PO4, MG, AMP |
| 2 | 69 | 0.30 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 1JP4 · Crystal Structure of an Enzyme Displaying both Inositol-Polyphosphate 1-Phosphatase and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Z1N4 · AlphaFold monomer V2.0 prediction for 3'(2'),5'-bisphosphate nucleotidase 1 (Q9Z1N4) · 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 Q9Z1N4
- Elsewhere: RCSB PDB 1JP4 · PDBe 1JP4 · UniProt Q9Z1N4
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