Research workbench
Crystal structure of D52N/R367Q cn-II mutant bound to datp and free phosphate
Analyse Crystal structure of D52N/R367Q cn-II mutant bound to datp and free phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OPK
- Type
- protein
- Length
- 472 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
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 472 | 44% 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 · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.71 | 0.90 | 33 | GOL |
| 2 | 404 | 0.67 | 0.80 | 40 | GOL, PO4, MG, DTP |
| 3 | 63 | 0.65 | 0.93 | 16 | empty |
| 4 | 168 | 0.61 | 0.83 | 24 | GOL |
| 5 | 298 | 0.56 | 0.76 | 26 | empty |
Compared structures
- 5OPK · Crystal structure of D52N/R367Q 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 5OPK · PDBe 5OPK · UniProt P49902
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