Research workbench
Rational discovery of a SOD1 tryptophan oxidation inhibitor with therapeutic potential for amyotrophic lateral sclerosis
Analyse Rational discovery of a SOD1 tryptophan oxidation inhibitor with therapeutic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A9O
- Type
- protein
- Length
- 1,512 residues
- Chains
- 10
- 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
- S4P, 6B3, ZN
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, I, J | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 154 | 8% helix, 39% strand | P00441 |
| G | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 127 | 4% helix, 48% strand | P00441 |
| H | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 7% helix, 40% strand | P00441 |
Ligands and binding sites
- S4P · Dihydrogen tetrasulfide · ligand · 3 copies · chains A, B, C, D, E, F
- 6B3 · 2'-[(6-oxo-5,6-dihydrophenanthridin-3-yl)carbamoyl][1,1'-biphenyl]-2-carboxylic acid · ligand · chains F, I
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D, E, F, H, I, J
- GOL · Glycerol · additive · 4 copies · chains A, B, G, C, D
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.74 | 0.80 | 69 | empty |
| 2 | 627 | 0.70 | 0.79 | 69 | S4P |
| 3 | 220 | 0.66 | 0.85 | 37 | DMS |
| 4 | 442 | 0.65 | 0.78 | 45 | empty |
| 5 | 323 | 0.64 | 0.80 | 46 | GOL |
Interfaces
13 interfaces between chains.
- C–D · 759 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 751 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 733 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 727 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 724 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 covalent (disulfide, covalent ligand).
Compared structures
- 6A9O · Rational discovery of a SOD1 tryptophan oxidation inhibitor with therapeutic potential… · 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 6A9O · PDBe 6A9O · UniProt P00441
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