Research workbench
Crystal structure of the Y34F mutant of saccharomyces cerevisiae manganese superoxide dismutase
Analyse Crystal structure of the Y34F mutant of saccharomyces cerevisiae manganese… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E4E
- Type
- protein
- Length
- 821 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
- MN
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 206 | 59% helix, 13% strand | P00447 |
| B | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 207 | 57% helix, 13% strand | P00447 |
| C | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 205 | 61% helix, 13% strand | P00447 |
| D | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 203 | 58% helix, 13% strand | P00447 |
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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.66 | 0.80 | 41 | empty |
| 2 | 327 | 0.63 | 0.79 | 36 | empty |
| 3 | 218 | 0.61 | 0.81 | 29 | empty |
| 4 | 123 | 0.59 | 0.85 | 26 | empty |
| 5 | 124 | 0.58 | 0.84 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1411 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1287 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1020 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1006 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 516 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 62 modified (methylation).
Compared structures
- 4E4E · Crystal Structure of the Y34F mutant of Saccharomyces cerevisiae Manganese Superoxide… · the same entry in another collection · chain D against D, TM-score 1.00
- P00447 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn], mitochondrial (P00447) · a predicted model of the same protein · chain D 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 4E4E · PDBe 4E4E · UniProt P00447
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