Research workbench
Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)
Analyse Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FB9
- Type
- protein
- Length
- 1,928 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Superoxide dismutase [Cu-Zn]
- EC
- 1.15.1.1
- UniProt
- P00441
- Ligands
- ZN, CU
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.7 · 4 distinct chains · 5% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, H, I, J, K, L | Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) | protein | 153 | 5% helix, 40% strand | P00441 |
| C, D | Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) | protein | 152 | 2% helix, 40% strand | P00441 |
| M | Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) | protein | 68 | 6% helix, 9% strand | P00441 |
| N | Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) | protein | 26 | 12% helix, 0% strand | P00441 |
Ligands and binding sites
- ZN · Zinc ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- CU · Copper (II) ion · metal · 6 copies · chains A, D, H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.78 | 0.80 | 118 | empty |
| 2 | 525 | 0.73 | 0.82 | 52 | empty |
| 3 | 769 | 0.73 | 0.78 | 72 | empty |
| 4 | 137 | 0.65 | 0.88 | 33 | empty |
| 5 | 316 | 0.62 | 0.79 | 54 | empty |
Interfaces
20 interfaces between chains.
- C–I · 772 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 727 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 727 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 4 hydrogen bonds · protein-protein
- H–L · 716 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
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 7FB9 · PDBe 7FB9 · UniProt P00441
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