MolNFT v1 · #127728 · protein
Staphylococcus aureus mn-dependent superoxide dismutase soda
5N56 · Superoxide dismutase [MN/FE] 1: “Staphylococcus aureus mn-dependent superoxide dismutase soda”. X-ray diffraction, 1 ligand (MN), 2 pockets (best druggability 0.55). MolNFT v1 #127728 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N56
- Type
- protein
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [MN/FE] 1
- EC
- 1.15.1.1
- UniProt
- Q2YT26
- Ligands
- MN
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase [MN/FE] 1 (EC 1.15.1.1) | protein | 198 | 55% helix, 13% strand | Q2YT26 |
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
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 | 174 | 0.55 | 0.80 | 21 | empty |
| 2 | 183 | 0.54 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5N56 · Staphylococcus aureus Mn-dependent superoxide dismutase SodA · the same entry in another collection · chain B against B, TM-score 1.00
- Q2YT26 · AlphaFold monomer V2.0 prediction for superoxide dismutase [MN/FE] 1 (Q2YT26) · 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 Q2YT26
- Elsewhere: RCSB PDB 5N56 · PDBe 5N56 · UniProt Q2YT26
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