MolNFT v1 · #86330 · protein
Structure of copper-zinc superoxide dismutase complexed with bicarbonate.
4B3E · Superoxide dismutase [cu-zn]: “Structure of copper-zinc superoxide dismutase complexed with bicarbonate.”. X-ray diffraction, 4 ligands (CU, ZN, CO3), 15 pockets (best druggability 0.81). MolNFT v1 #86330 on GenesisL1: 3D structure…
- PDB
- 4B3E
- Type
- protein
- Length
- 1,530 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
- CU, ZN, CO3, SO4
- Pockets
- 15 · best druggability 0.81
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 | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 6% helix, 41% strand | P00441 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CO3 · Carbonate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- SO4 · Sulfate ion · ion · 5 copies · chains F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.81 | 0.83 | 82 | CO3 |
| 2 | 917 | 0.76 | 0.79 | 94 | SO4 |
| 3 | 878 | 0.72 | 0.77 | 95 | CO3 |
| 4 | 418 | 0.71 | 0.82 | 71 | empty |
| 5 | 147 | 0.66 | 0.87 | 28 | empty |
Interfaces
13 interfaces between chains.
- D–I · 744 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 732 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 730 Ų buried · 5 hydrogen bonds · protein-protein
- B–G · 723 Ų buried · 4 hydrogen bonds · protein-protein
- E–J · 721 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4B3E · Structure of copper-zinc superoxide dismutase complexed with bicarbonate. · 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 4B3E · PDBe 4B3E · UniProt P00441
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