MolNFT v1 · #146301 · protein
Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X in the active state, northeast structural genomics target
6DDH · Cytosolic purine 5'-nucleotidase: “Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X in the active state, northeast structural…”. X-ray diffraction, 1 ligand (IMP), 6 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 6DDH
- 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
- IMP
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 473 | 44% helix, 18% strand | P49902 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 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 | 112 | 0.72 | 0.93 | 31 | empty |
| 2 | 51 | 0.69 | 0.97 | 14 | empty |
| 3 | 401 | 0.64 | 0.78 | 45 | IMP |
| 4 | 168 | 0.62 | 0.84 | 23 | empty |
| 5 | 269 | 0.59 | 0.78 | 27 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6DDH · Crystal structure of the double mutant (D52N/R367Q) 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 6DDH · PDBe 6DDH · UniProt P49902
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