Research workbench
Superoxide reductase (neelaredoxin) from archaeoglobus fulgidus
Analyse Superoxide reductase (neelaredoxin) from archaeoglobus fulgidus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BGL
- Type
- protein
- Length
- 495 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide reductase
- UniProt
- O29903
- Ligands
- FE
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Superoxide reductase | protein | 124 | 0% helix, 54% strand | O29903 |
| D | Superoxide reductase | protein | 123 | 0% helix, 54% strand | O29903 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.85 | 0.97 | 43 | GOL |
| 2 | 250 | 0.84 | 0.96 | 42 | GOL |
| 3 | 137 | 0.45 | 0.77 | 24 | empty |
| 4 | 150 | 0.45 | 0.76 | 32 | empty |
| 5 | 98 | 0.39 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1221 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1213 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 912 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 911 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 468 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4BGL · Superoxide reductase (Neelaredoxin) from Archaeoglobus fulgidus · the same entry in another collection · chain A against A, TM-score 1.00
- O29903 · AlphaFold monomer V2.0 prediction for putative superoxide reductase (O29903) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 O29903
- Elsewhere: RCSB PDB 4BGL · PDBe 4BGL · UniProt O29903
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