MolNFT v2 · #215139 · protein
Superoxide dismutase
8KB3 · Superoxide dismutase [Mn]: “Superoxide dismutase”. X-ray diffraction at 1.62, 2 ligands (MN, SO4), 2 pockets (best druggability 0.50). MolNFT v2 #215139 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8KB3
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.62
- Source
- Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
- Molecule
- Superoxide dismutase [Mn]
- EC
- 1.15.1.1
- UniProt
- P43019
- Ligands
- MN, SO4
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · resolution 1.62 · 1 distinct chain · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase [Mn] (EC 1.15.1.1) | protein | 206 | 57% helix, 12% strand | P43019 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.50 | 0.79 | 21 | empty |
| 2 | 134 | 0.49 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- P43019 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn] (P43019) · 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 P43019
- Elsewhere: RCSB PDB 8KB3 · PDBe 8KB3 · UniProt P43019
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.