Research workbench
Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with guanosine monophosphate and diadenosine tetraphosphate
Analyse Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XJC
- Type
- protein
- Length
- 463 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
- 5GP, B4P, MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 463 | 42% helix, 17% strand | P49902 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · chains A
- B4P · Bis(adenosine)-5'-tetraphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.71 | 0.91 | 28 | GOL |
| 2 | 449 | 0.66 | 0.79 | 48 | 5GP, GOL, MG |
| 3 | 172 | 0.62 | 0.84 | 25 | GOL |
| 4 | 241 | 0.61 | 0.81 | 26 | empty |
| 5 | 149 | 0.50 | 0.78 | 18 | empty |
Compared structures
- 2XJC · Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with… · 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 0.93
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 2XJC · PDBe 2XJC · UniProt P49902
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