MolNFT v1 · #70402 · protein
The X-ray structure of iron superoxide dismutase from pseudoalteromonas haloplanktis (crystal form II)
3LJF: “The X-ray structure of iron superoxide dismutase from pseudoalteromonas haloplanktis (crystal form II)”. X-ray diffraction, 2 ligands (GLC, FE), 4 pockets (best druggability 0.61). MolNFT v1 #70402 on GenesisL1: 3D structure…
- PDB
- 3LJF
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- 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
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Iron superoxide dismutase (EC 1.15.1.1) | protein | 192 | 54% helix, 12% strand | P84612 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.61 | 0.82 | 23 | empty |
| 2 | 196 | 0.61 | 0.82 | 21 | empty |
| 3 | 208 | 0.60 | 0.81 | 21 | empty |
| 4 | 201 | 0.59 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1031 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1027 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LJF · The X-ray structure of iron superoxide dismutase from Pseudoalteromonas haloplanktis… · 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 3LJF · PDBe 3LJF · UniProt P84612
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