Research workbench
Superoxide dismutase mutant with lys 136 replaced by glu, cys 6 replaced by ala and cys 111 replaced by ser (K136E, C6A, C111S)
Analyse Superoxide dismutase mutant with lys 136 replaced by glu, cys 6 replaced by ala… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FUN
- Type
- protein
- Length
- 1,530 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P00441
- Ligands
- CU, ZN, SO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, B, G, C, H, D, I, E, J | Superoxide dismutase (EC 1.15.1.1) | protein | 153 | 5% helix, 39% strand | P00441 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 10 copies · chains A, F, B, G, C, H, D, I, E, J
- ZN · Zinc ion · metal · 10 copies · chains A, F, B, G, C, H, D, I, E, J
- SO4 · Sulfate ion · ion · chains F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.80 | 0.82 | 97 | empty |
| 2 | 444 | 0.75 | 0.84 | 57 | empty |
| 3 | 238 | 0.65 | 0.83 | 36 | SO4 |
| 4 | 184 | 0.63 | 0.84 | 29 | empty |
| 5 | 520 | 0.62 | 0.75 | 52 | empty |
Interfaces
14 interfaces between chains.
- A–F · 712 Ų buried · 4 hydrogen bonds · protein-protein
- E–J · 711 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 678 Ų buried · 4 hydrogen bonds · protein-protein
- D–I · 676 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 675 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1FUN · Superoxide dismutase mutant with lys 136 replaced by glu, cys 6 replaced by ala and cys… · the same entry in another collection · chain F against F, 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 P00441
- Elsewhere: RCSB PDB 1FUN · PDBe 1FUN · UniProt P00441
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