MolNFT v1 · #146319 · protein
Crystal structure of the double mutant (D52N/R238W) of NT5C2-537X in the active state, northeast structural genomics target
6DDZ · Cytosolic purine 5'-nucleotidase: “Crystal structure of the double mutant (D52N/R238W) of NT5C2-537X in the active state, northeast structural…”. X-ray diffraction, 3 ligands (ATP, MG, PO4), 6 pockets (best druggability 0.68).…
- PDB
- 6DDZ
- Type
- protein
- Length
- 473 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
- ATP, MG, PO4
- Pockets
- 6 · best druggability 0.68
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 | 473 | 43% helix, 17% strand | P49902 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.68 | 0.90 | 28 | empty |
| 2 | 367 | 0.67 | 0.81 | 42 | PO4, MG |
| 3 | 178 | 0.65 | 0.85 | 22 | empty |
| 4 | 256 | 0.59 | 0.79 | 27 | empty |
| 5 | 154 | 0.52 | 0.79 | 15 | empty |
Compared structures
- 6DDZ · Crystal structure of the double mutant (D52N/R238W) of NT5C2-537X in the active state… · 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 6DDZ · PDBe 6DDZ · UniProt P49902
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.