MolNFT v1 · #4602 · protein
Cloning, sequence, and crystallographic structure of recombinant iron superoxide dismutase from pseudomonas ovalis
1DT0: “Cloning, sequence, and crystallographic structure of recombinant iron superoxide dismutase from pseudomonas…”. X-ray diffraction, 1 ligand (FE), 2 pockets (best druggability 0.55). MolNFT v1 #4602 on GenesisL1: 3D structure, binding…
- PDB
- 1DT0
- Type
- protein
- Length
- 589 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P09223
- Ligands
- FE
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase (EC 1.15.1.1) | protein | 197 | 50% helix, 12% strand | P09223 |
| C | Superoxide dismutase (EC 1.15.1.1) | protein | 195 | 52% helix, 12% strand | P09223 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
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 | 182 | 0.55 | 0.80 | 20 | empty |
| 2 | 192 | 0.52 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 917 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1DT0 · Cloning, sequence, and crystallographic structure of recombinant iron superoxide… · the same entry in another collection · chain A against A, TM-score 1.00
- P09223 · AlphaFold monomer V2.0 prediction for superoxide dismutase [fe] (P09223) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P09223
- Elsewhere: RCSB PDB 1DT0 · PDBe 1DT0 · UniProt P09223
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