Research workbench
A4V mutant of human SOD1 with ebselen derivative 4
Analyse A4V mutant of human SOD1 with ebselen derivative 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SPI
- Type
- protein
- Length
- 1,836 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [cu-zn]
- EC
- 1.15.1.1
- UniProt
- P00441
- Ligands
- LQW, ZN, SO4
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 6% helix, 41% strand | P00441 |
Ligands and binding sites
- LQW · ~{N}-[(4-chlorophenyl)methyl]-2-selanyl-benzamide · ligand · 12 copies · chains A, B, K, C, I, D, L, E, G, F, H, J
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D, F, E, G, H, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.78 | 0.80 | 108 | SO4 |
| 2 | 821 | 0.71 | 0.77 | 112 | empty |
| 3 | 586 | 0.70 | 0.79 | 103 | empty |
| 4 | 739 | 0.69 | 0.77 | 66 | SO4 |
| 5 | 638 | 0.68 | 0.77 | 80 | empty |
Interfaces
21 interfaces between chains.
- A–J · 773 Ų buried · 7 hydrogen bonds · protein-protein
- B–K · 768 Ų buried · 5 hydrogen bonds · protein-protein
- D–L · 753 Ų buried · 5 hydrogen bonds · protein-protein
- C–I · 748 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 738 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent, 12 disulfide (covalent ligand, disulfide).
Compared structures
- 6SPI · A4V mutant of human SOD1 with ebselen derivative 4 · the same entry in another collection · chain A 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 P00441
- Elsewhere: RCSB PDB 6SPI · PDBe 6SPI · UniProt P00441
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