Research workbench
Crystal structure of the peroxide-bound manganese superoxide dismutase.
Analyse Crystal structure of the peroxide-bound manganese superoxide dismutase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K9S
- Type
- protein
- Length
- 820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [mn]
- EC
- 1.15.1.1
- UniProt
- P00448
- Ligands
- PEO, MN
- Pockets
- 9 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Superoxide dismutase [mn] (EC 1.15.1.1) | protein | 205 | 52% helix, 12% strand | P00448 |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 3 copies · chains B, C, D
- 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.55 | 0.80 | 18 | empty |
| 2 | 170 | 0.54 | 0.80 | 18 | empty |
| 3 | 176 | 0.52 | 0.78 | 21 | empty |
| 4 | 235 | 0.51 | 0.75 | 29 | empty |
| 5 | 166 | 0.51 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 918 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 916 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3K9S · Crystal structure of the peroxide-bound manganese superoxide dismutase. · 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 3K9S · PDBe 3K9S · UniProt P00448
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