MolNFT v1 · #120355 · protein
Discovery of a compound that activates SIRT3 to deacetylate manganese superoxide dismutase
5GXO · Superoxide dismutase [mn], mitochondrial: “Discovery of a compound that activates SIRT3 to deacetylate manganese superoxide dismutase”. X-ray diffraction, 1 ligand (MN), 1 pocket (best druggability 0.48). MolNFT v1 #120355 on…
- PDB
- 5GXO
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [mn], mitochondrial
- EC
- 1.15.1.1
- UniProt
- P04179
- Ligands
- MN
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 197 | 57% helix, 13% strand | P04179 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.48 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 281 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 5GXO · Discovery of a compound that activates SIRT3 to deacetylate Manganese Superoxide Dismutase · the same entry in another collection · chain A against A, TM-score 1.00
- P04179 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn], mitochondrial (P04179) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P04179
- Elsewhere: RCSB PDB 5GXO · PDBe 5GXO · UniProt P04179
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