MolNFT v1 · #41075 · protein
Crystal structure of human cytosolic 5'-nucleotidase II in complex with beryllium trifluoride
2JCM · Cytosolic purine 5'-nucleotidase: “Crystal structure of human cytosolic 5'-nucleotidase II in complex with beryllium trifluoride”. X-ray diffraction, 3 ligands (MG, SO4, UNX), 5 pockets (best druggability 0.67). MolNFT v1 #41075 on…
- PDB
- 2JCM
- Type
- protein
- Length
- 467 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
- MG, SO4, UNX
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 467 | 42% helix, 18% strand | P49902 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- UNX · Unknown atom or ion · ion · 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 | 104 | 0.67 | 0.90 | 28 | empty |
| 2 | 170 | 0.64 | 0.85 | 23 | empty |
| 3 | 426 | 0.62 | 0.77 | 37 | empty |
| 4 | 284 | 0.57 | 0.77 | 26 | empty |
| 5 | 154 | 0.53 | 0.79 | 16 | empty |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 2JCM · Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with beryllium… · 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 2JCM · PDBe 2JCM · UniProt P49902
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