MolNFT v1 · #74130 · protein
Crystal structure of 5'-nucleotidase SDT1 from saccharomyces cerevisiae
3ONN · Protein SSM1: “Crystal structure of 5'-nucleotidase SDT1 from saccharomyces cerevisiae”. X-ray diffraction, 3 ligands (MG, IOD, PO4), 2 pockets (best druggability 0.79). MolNFT v1 #74130 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ONN
- Type
- protein
- Length
- 249 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SSM1
- UniProt
- P53078
- Ligands
- MG, IOD, PO4
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein SSM1 | protein | 249 | 47% helix, 10% strand | P53078 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- IOD · Iodide ion · ion · 4 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.79 | 0.95 | 33 | PO4 |
| 2 | 171 | 0.53 | 0.79 | 36 | GOL |
Compared structures
- 3ONN · Crystal structure of 5'-nucleotidase SDT1 from saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P53078 · AlphaFold monomer V2.0 prediction for suppressor of disruption of tfiis (P53078) · 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 P53078
- Elsewhere: RCSB PDB 3ONN · PDBe 3ONN · UniProt P53078
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