Research workbench
Structure and properties of the atypical iron superoxide dismutase from methanobacterium thermoautotrophicum
Analyse Structure and properties of the atypical iron superoxide dismutase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MA1
- Type
- protein
- Length
- 1,206 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P18868
- Ligands
- FE
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Superoxide dismutase (EC 1.15.1.1) | protein | 201 | 51% helix, 11% strand | P18868 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.82 | 0.96 | 34 | empty |
| 2 | 730 | 0.74 | 0.80 | 68 | empty |
| 3 | 319 | 0.59 | 0.77 | 38 | empty |
| 4 | 295 | 0.59 | 0.78 | 40 | empty |
| 5 | 253 | 0.57 | 0.78 | 32 | empty |
Interfaces
10 interfaces between chains.
- D–F · 2823 Ų buried · 45 hydrogen bonds · protein-protein
- C–E · 2812 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 949 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 934 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 933 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1MA1 · Structure and properties of the atypical iron superoxide dismutase from Methanobacterium… · the same entry in another collection · chain B against B, TM-score 1.00
- P18868 · AlphaFold monomer V2.0 prediction for superoxide dismutase [fe] (P18868) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P18868
- Elsewhere: RCSB PDB 1MA1 · PDBe 1MA1 · UniProt P18868
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