Research workbench
X-ray structure of the IRON/MANGANESE cambialistic superoxide dismutase from streptococcus thermophilus
Analyse X-ray structure of the IRON/MANGANESE cambialistic superoxide dismutase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YIO
- Type
- protein
- Length
- 403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- Q5M4Z1
- Ligands
- FE, SO4
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superoxide dismutase (EC 1.15.1.1) | protein | 202 | 57% helix, 11% strand | Q5M4Z1 |
| B | Superoxide dismutase (EC 1.15.1.1) | protein | 201 | 57% helix, 11% strand | Q5M4Z1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.56 | 0.80 | 27 | empty |
| 2 | 173 | 0.52 | 0.79 | 18 | empty |
| 3 | 148 | 0.46 | 0.76 | 22 | empty |
| 4 | 126 | 0.44 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 991 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4YIO · X-ray structure of the iron/manganese cambialistic superoxide dismutase from… · the same entry in another collection · 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 Q5M4Z1
- Elsewhere: RCSB PDB 4YIO · PDBe 4YIO · UniProt Q5M4Z1
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