MolNFT v1 · #146305 · protein
Crystal structure of the single mutant (D52N) of NT5C2-Q523X in the basal state
6DDL · Cytosolic purine 5'-nucleotidase: “Crystal structure of the single mutant (D52N) of NT5C2-Q523X in the basal state”. X-ray diffraction, 1 ligand (PO4), 11 pockets (best druggability 0.83). MolNFT v1 #146305 on GenesisL1: 3D…
- PDB
- 6DDL
- Type
- protein
- Length
- 933 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
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 464 | 40% helix, 18% strand | P49902 |
| B | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 469 | 40% helix, 18% strand | P49902 |
Ligands and binding sites
- 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
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.83 | 0.84 | 93 | PO4 |
| 2 | 1084 | 0.82 | 0.83 | 92 | PO4 |
| 3 | 404 | 0.78 | 0.87 | 47 | empty |
| 4 | 254 | 0.62 | 0.81 | 29 | PO4 |
| 5 | 256 | 0.59 | 0.79 | 39 | PO4 |
Interfaces
1 interface between chains.
- A–B · 5488 Ų buried · 74 hydrogen bonds · protein-protein
Compared structures
- 6DDL · Crystal structure of the single mutant (D52N) of NT5C2-Q523X 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 6DDL · PDBe 6DDL · UniProt P49902
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