Research workbench
Crystal structure of the K182R, A183P mutant manganese superoxide dismutase from sacchromyces cerevisiae
Analyse Crystal structure of the K182R, A183P mutant 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
- 4F6E
- Type
- protein
- Length
- 824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [mn], mitochondrial
- EC
- 1.15.1.1
- UniProt
- P00447
- Ligands
- MLY, MN
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 207 | 61% helix, 13% strand | P00447 |
| B, D | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 205 | 60% helix, 13% strand | P00447 |
Ligands and binding sites
- MLY · N-dimethyl-lysine · ligand · chains D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.71 | 0.80 | 63 | empty |
| 2 | 311 | 0.65 | 0.80 | 39 | empty |
| 3 | 136 | 0.54 | 0.81 | 24 | empty |
| 4 | 175 | 0.54 | 0.79 | 21 | empty |
| 5 | 178 | 0.52 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1386 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1378 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 973 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 958 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 518 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 modified, 1 covalent (methylation, covalent ligand).
Compared structures
- 4F6E · Crystal Structure of the K182R, A183P mutant manganese superoxide dismutase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P00447 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn], mitochondrial (P00447) · a predicted model of the same protein · chain C 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 P00447
- Elsewhere: RCSB PDB 4F6E · PDBe 4F6E · UniProt P00447
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