MolNFT v1 · #41260 · protein
X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from desulfoarculus baarsii
2JI3 · Desulfoferrodoxin: “X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from desulfoarculus…”. X-ray diffraction, 4 ligands (FE, CA, PER), 1 pocket (best druggability 0.26). MolNFT v1 #41260 on…
- PDB
- 2JI3
- Type
- protein
- Length
- 502 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desulfoferrodoxin
- EC
- 1.15.1.2
- UniProt
- Q46495
- Ligands
- FE, CA, PER, NO3
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Desulfoferrodoxin (EC 1.15.1.2) | protein | 126 | 3% helix, 46% strand | Q46495 |
| B, D | Desulfoferrodoxin (EC 1.15.1.2) | protein | 125 | 3% helix, 48% strand | Q46495 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PER · Peroxide ion · ion · 3 copies · chains B, C, D
- NO3 · Nitrate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.26 | 0.71 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1658 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1642 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2JI3 · X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q46495 · AlphaFold monomer V2.0 prediction for desulfoferrodoxin (Q46495) · a predicted model of the same protein · 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 Q46495
- Elsewhere: RCSB PDB 2JI3 · PDBe 2JI3 · UniProt Q46495
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