Research workbench
Crystal structure analysis of the E. COLI manganese superoxide dismutase Y34F mutant
Analyse Crystal structure analysis of the E. COLI manganese superoxide dismutase Y34F… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EN5
- Type
- protein
- Length
- 820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P00448
- Ligands
- MN
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Manganese superoxide dismutase (EC 1.15.1.1) | protein | 205 | 53% helix, 12% strand | P00448 |
Ligands and binding sites
- MN · Manganese (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.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.63 | 0.76 | 70 | empty |
| 2 | 180 | 0.56 | 0.80 | 25 | empty |
| 3 | 206 | 0.55 | 0.79 | 22 | empty |
| 4 | 175 | 0.54 | 0.80 | 20 | empty |
| 5 | 164 | 0.52 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 917 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 912 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 221 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1EN5 · Crystal structure analysis of the E. COLI manganese superoxide dismutase Y34F mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P00448 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn] (P00448) · a predicted model of the same protein · chain A 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 P00448
- Elsewhere: RCSB PDB 1EN5 · PDBe 1EN5 · UniProt P00448
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