Research workbench
Crystal structure of SOD2 from saccharomyces cerevisiae
Analyse Crystal structure of SOD2 from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LSU
- Type
- protein
- Length
- 826 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, NA
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 206 | 61% helix, 13% strand | P00447 |
| B, D | Superoxide dismutase [mn], mitochondrial (EC 1.15.1.1) | protein | 207 | 61% helix, 13% strand | P00447 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C
- GOL · Glycerol · additive · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.69 | 0.80 | 59 | empty |
| 2 | 426 | 0.68 | 0.80 | 45 | empty |
| 3 | 74 | 0.61 | 0.90 | 21 | empty |
| 4 | 169 | 0.53 | 0.79 | 28 | empty |
| 5 | 78 | 0.51 | 0.84 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1463 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1424 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1030 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 516 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (methylation).
Compared structures
- 3LSU · Crystal Structure of SOD2 from Saccharomyces cerevisiae · 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 B 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 3LSU · PDBe 3LSU · UniProt P00447
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.