MolNFT v1 · #52894 · protein
Human 3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, PO4 and magnesium
2WEF · 3'(2')\, 5'-bisphosphate nucleotidase 1: “Human 3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, PO4 and magnesium”. X-ray diffraction, 3 ligands (AMP, MG, PO4), 4 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 2WEF
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3'(2')\, 5'-bisphosphate nucleotidase 1
- EC
- 3.1.3.7
- UniProt
- O95861
- Ligands
- AMP, MG, PO4
- Pockets
- 4 · best druggability 0.72
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 1 (EC 3.1.3.7) | protein | 303 | 35% helix, 23% strand | O95861 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.72 | 0.87 | 35 | MG, PO4, AMP |
| 2 | 58 | 0.41 | 0.81 | 17 | empty |
| 3 | 56 | 0.36 | 0.79 | 14 | empty |
| 4 | 60 | 0.29 | 0.74 | 16 | empty |
Compared structures
- 2WEF · Human 3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, PO4 and… · the same entry in another collection · chain A against A, TM-score 1.00
- O95861 · AlphaFold monomer V2.0 prediction for 3'(2'),5'-bisphosphate nucleotidase 1 (O95861) · 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 O95861
- Elsewhere: RCSB PDB 2WEF · PDBe 2WEF · UniProt O95861
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