MolNFT v1 · #129618 · protein
Crystal structure of D52N/R238W cn-II mutant bound to datp and free phosphate
5OPM · Cytosolic purine 5'-nucleotidase: “Crystal structure of D52N/R238W cn-II mutant bound to datp and free phosphate”. X-ray diffraction, 3 ligands (DTP, MG, PO4), 5 pockets (best druggability 0.67). MolNFT v1 #129618 on GenesisL1: 3D…
- PDB
- 5OPM
- Type
- protein
- Length
- 469 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic purine 5'-nucleotidase
- EC
- 3.1.3.5
- UniProt
- P49902
- Ligands
- DTP, MG, PO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 469 | 43% helix, 17% strand | P49902 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.67 | 0.89 | 29 | empty |
| 2 | 326 | 0.65 | 0.80 | 40 | PO4, DTP, GOL |
| 3 | 170 | 0.61 | 0.83 | 24 | empty |
| 4 | 315 | 0.61 | 0.78 | 26 | GOL |
| 5 | 135 | 0.50 | 0.78 | 15 | empty |
Compared structures
- 5OPM · Crystal structure of D52N/R238W cN-II mutant bound to dATP and free phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P49902 · AlphaFold monomer V2.0 prediction for cytosolic purine 5'-nucleotidase (P49902) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P49902
- Elsewhere: RCSB PDB 5OPM · PDBe 5OPM · UniProt P49902
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