Research workbench
Structure of human SOD1 complexed with isoproteranol in C2221 space group
Analyse Structure of human SOD1 complexed with isoproteranol in C2221 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YTU
- Type
- protein
- Length
- 1,508 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, 5FW, TAM, ZN
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, B, C, D, F | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 154 | 8% helix, 39% strand | P00441 |
| E | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 155 | 6% helix, 39% strand | P00441 |
| G | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 125 | 6% helix, 49% strand | P00441 |
| I, J | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 152 | 8% helix, 40% strand | P00441 |
Ligands and binding sites
- S4P · Dihydrogen tetrasulfide · ligand · 3 copies · chains A, H, B, C, D, E
- 5FW · Isoprenaline · ligand · chains A
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- ZN · Zinc ion · metal · 9 copies · chains A, H, B, C, D, E, F, I, J
- GOL · Glycerol · additive · 2 copies · chains H, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.81 | 0.83 | 116 | S4P |
| 2 | 147 | 0.67 | 0.88 | 32 | empty |
| 3 | 264 | 0.66 | 0.83 | 43 | empty |
| 4 | 181 | 0.65 | 0.85 | 34 | empty |
| 5 | 332 | 0.63 | 0.79 | 46 | GOL |
Interfaces
13 interfaces between chains.
- A–H · 805 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 782 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 746 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 737 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 730 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5YTU · Structure of human SOD1 complexed with isoproteranol in C2221 space group · 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 5YTU · PDBe 5YTU · UniProt P00441
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