Research workbench
Iron superoxide dismutase (fe-sod) from the hyperthermophile sulfolobus solfataricus. 2.3 a resolution structure of recombinant protein with a covalently modified tyrosine in the active site.
Analyse Iron superoxide dismutase (fe-sod) from the hyperthermophile sulfolobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WB8
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [fe]
- EC
- 1.15.1.1
- UniProt
- P80857
- Ligands
- PMS, FE
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase [fe] (EC 1.15.1.1) | protein | 205 | 52% helix, 12% strand | P80857 |
Ligands and binding sites
- PMS · phenylmethanesulfonic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.57 | 0.78 | 28 | PMS |
| 2 | 294 | 0.56 | 0.76 | 32 | PMS |
| 3 | 50 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 943 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1WB8 · Iron Superoxide Dismutase (FE-SOD) from the Hyperthermophile SULFOLOBUS SOLFATARICUS. 2.3… · the same entry in another collection · chain A against A, TM-score 1.00
- P80857 · AlphaFold monomer V2.0 prediction for superoxide dismutase [fe] (P80857) · 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 P80857
- Elsewhere: RCSB PDB 1WB8 · PDBe 1WB8 · UniProt P80857
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