MolNFT v1 · #91211 · protein
Crystal structure of the K182R, A183P mutant manganese superoxide dismutase from sacchromyces cerevisiae
4F6E · Superoxide dismutase [mn], mitochondrial: “Crystal structure of the K182R, A183P mutant manganese superoxide dismutase from sacchromyces cerevisiae”. X-ray diffraction, 2 ligands (MLY, MN), 11 pockets (best druggability 0.71).…
- 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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