Research workbench
Crystal structure of the D52N variant of cytosolic 5'- nucleotidase II with a covalently modified ASN52
Analyse Crystal structure of the D52N variant of cytosolic 5'- nucleotidase II with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XJF
- Type
- protein
- Length
- 462 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
- DG2
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 462 | 43% helix, 18% strand | P49902 |
Ligands and binding sites
- DG2 · (2R)-2,3-diphosphoglyceric acid · ligand · chains A
- GOL · Glycerol · additive · 3 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 | 120 | 0.71 | 0.92 | 28 | empty |
| 2 | 188 | 0.64 | 0.84 | 22 | empty |
| 3 | 318 | 0.61 | 0.79 | 36 | GOL |
| 4 | 252 | 0.55 | 0.77 | 25 | empty |
| 5 | 147 | 0.51 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 2XJF · Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II with a covalently… · 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 0.93
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 2XJF · PDBe 2XJF · UniProt P49902
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