Research workbench
X-ray structure of the iron superoxide dismutase from pseudoalteromonas haloplanktis in complex with sodium azide
Analyse X-ray structure of the iron superoxide dismutase from pseudoalteromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LJ9
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P84612
- Ligands
- GLC, FE, AZI
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Iron superoxide dismutase (EC 1.15.1.1) | protein | 192 | 52% helix, 12% strand | P84612 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- AZI · Azide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.61 | 0.83 | 21 | empty |
| 2 | 193 | 0.59 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1023 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3LJ9 · X-ray structure of the iron superoxide dismutase from pseudoalteromonas haloplanktis in… · the same entry in another collection · chain A against A, TM-score 1.00
- P84612 · AlphaFold monomer V2.0 prediction for superoxide dismutase [fe] (P84612) · 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 P84612
- Elsewhere: RCSB PDB 3LJ9 · PDBe 3LJ9 · UniProt P84612
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