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X-ray structure of wild-type superoxide reductase from desulfoarculus baarsii

Analyse X-ray structure of wild-type superoxide reductase from desulfoarculus baarsii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2JI1
Type
protein
Length
500 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, FE2

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 49% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DDesulfoferrodoxin (EC 1.15.1.2)protein1253% helix, 49% strandQ46495

Ligands and binding sites

  • FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
  • CA · Calcium ion · metal · 4 copies · chains A, B, C, D
  • FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

3 interfaces between chains.

  • A–B · 1624 Ų buried · 33 hydrogen bonds · protein-protein
  • C–D · 1595 Ų buried · 30 hydrogen bonds · protein-protein
  • A–D · 36 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

  • 2JI1 · X-ray structure of wild-type superoxide reductase from Desulfoarculus baarsii · 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

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