Research workbench
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho- enzyme intermediate analog with beryllium fluoride
Analyse X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho- enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G07
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic 5'-nucleotidase III
- EC
- 3.1.1.5
- UniProt
- Q9D020
- Ligands
- MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytosolic 5'-nucleotidase III (EC 3.1.1.5) | protein | 291 | 47% helix, 20% strand | Q9D020 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.78 | 0.83 | 57 | empty |
| 2 | 600 | 0.78 | 0.84 | 54 | empty |
| 3 | 1084 | 0.75 | 0.78 | 71 | empty |
| 4 | 50 | 0.33 | 0.78 | 15 | empty |
| 5 | 51 | 0.27 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 446 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered, nonstandard).
Compared structures
- 2G07 · X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho-enzyme intermediate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9D020 · AlphaFold monomer V2.0 prediction for cytosolic 5'-nucleotidase 3A (Q9D020) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9D020
- Elsewhere: RCSB PDB 2G07 · PDBe 2G07 · UniProt Q9D020
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