MolNFT v1 · #146296 · protein
Crystal structure of the single mutant (D52N) of NT5C2-537X in the basal state, northeast structural genomics consortium target
6DDC · Cytosolic purine 5'-nucleotidase: “Crystal structure of the single mutant (D52N) of NT5C2-537X in the basal state, northeast structural genomics…”. X-ray diffraction, 2 ligands (MG, PO4), 12 pockets (best druggability 0.83). MolNFT…
- PDB
- 6DDC
- Type
- protein
- Length
- 949 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
- MG, PO4
- Pockets
- 12 · best druggability 0.83
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 | 475 | 38% helix, 18% strand | P49902 |
| B | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 474 | 39% helix, 18% strand | P49902 |
Ligands and binding sites
- MG · Magnesium 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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.83 | 0.84 | 96 | PO4 |
| 2 | 157 | 0.79 | 0.96 | 24 | empty |
| 3 | 1021 | 0.79 | 0.80 | 78 | PO4 |
| 4 | 718 | 0.79 | 0.83 | 73 | MG, PO4 |
| 5 | 239 | 0.61 | 0.81 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 5188 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 6DDC · Crystal structure of the single mutant (D52N) of NT5C2-537X in the basal state, Northeast… · 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 6DDC · PDBe 6DDC · UniProt P49902
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