MolNFT v1 · #146304 · protein
Crystal structure of the double mutant (D52N/R367Q) of the full-length NT5C2 in the basal state
6DDK · Cytosolic purine 5'-nucleotidase: “Crystal structure of the double mutant (D52N/R367Q) of the full-length NT5C2 in the basal state”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.70). MolNFT v1 #146304 on…
- PDB
- 6DDK
- Type
- protein
- Length
- 982 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
- PO4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 500 | 38% helix, 17% strand | P49902 |
| B | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 482 | 40% helix, 18% strand | P49902 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.70 | 0.78 | 68 | empty |
| 2 | 669 | 0.68 | 0.77 | 65 | empty |
| 3 | 372 | 0.65 | 0.79 | 54 | empty |
| 4 | 305 | 0.65 | 0.81 | 44 | empty |
| 5 | 375 | 0.63 | 0.77 | 38 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1338 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6DDK · Crystal structure of the double mutant (D52N/R367Q) of the full-length NT5C2 in the basal… · 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 B against A, TM-score 0.96
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 6DDK · PDBe 6DDK · UniProt P49902
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