MolNFT v1 · #148848 · protein
Human cytosolic 5'-nucleotidase II soaked with 5MM3-phenyl-N-(9H- purin-6-YL)BENZAMIDE
6FIR · Cytosolic purine 5'-nucleotidase: “Human cytosolic 5'-nucleotidase II soaked with 5MM3-phenyl-N-(9H- purin-6-YL)BENZAMIDE”. X-ray diffraction, 2 ligands (MG, SO4), 6 pockets (best druggability 0.69). MolNFT v1 #148848 on GenesisL1…
- PDB
- 6FIR
- Type
- protein
- Length
- 475 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
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 475 | 45% helix, 17% strand | P49902 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 7 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.69 | 0.90 | 26 | GOL |
| 2 | 462 | 0.67 | 0.79 | 45 | MG, SO4 |
| 3 | 152 | 0.63 | 0.86 | 27 | GOL |
| 4 | 313 | 0.63 | 0.79 | 28 | empty |
| 5 | 161 | 0.49 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6FIR · Human cytosolic 5'-nucleotidase II soaked with 5mM3-Phenyl-N-(9H-purin-6-yl)benzamide · 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 6FIR · PDBe 6FIR · UniProt P49902
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