Research workbench
Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X in the basal state, northeast structural genomics consortium target
Analyse Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X in the basal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DDB
- Type
- protein
- Length
- 934 residues
- Chains
- 2
- 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
- MN, PO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 467 | 39% helix, 18% strand | P49902 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.83 | 0.84 | 92 | PO4 |
| 2 | 1018 | 0.83 | 0.84 | 92 | PO4 |
| 3 | 1132 | 0.79 | 0.81 | 107 | MN, PO4 |
| 4 | 342 | 0.65 | 0.80 | 51 | empty |
| 5 | 336 | 0.65 | 0.80 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 4499 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 6DDB · Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X in the basal 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 0.98
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 6DDB · PDBe 6DDB · UniProt P49902
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.