MolNFT v1 · #50891 · protein
Determination and analysis of the 2 ångström structure of copper, zinc superoxide dismutase
2SOD · COPPER,ZINC superoxide dismutase: “Determination and analysis of the 2 ångström structure of copper, zinc superoxide dismutase”. X-ray diffraction, 3 ligands (ACE, CU, ZN), 3 pockets (best druggability 0.72). MolNFT v1 #50891 on…
- PDB
- 2SOD
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COPPER,ZINC superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P00442
- Ligands
- ACE, CU, ZN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, Y, B, G | COPPER,ZINC superoxide dismutase (EC 1.15.1.1) | protein | 151 | 2% helix, 42% strand | P00442 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains O, Y, B, G
- CU · Copper (II) ion · metal · 4 copies · chains O, Y, B, G
- ZN · Zinc ion · metal · 4 copies · chains O, Y, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.72 | 0.76 | 97 | empty |
| 2 | 145 | 0.44 | 0.76 | 24 | ACE |
| 3 | 96 | 0.35 | 0.74 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–G · 695 Ų buried · 4 hydrogen bonds · protein-protein
- O–Y · 659 Ų buried · 7 hydrogen bonds · protein-protein
- O–B · 79 Ų buried · 1 hydrogen bond · protein-protein
- Y–G · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 2SOD · Determination and analysis of the 2 ångström structure of copper, zinc superoxide… · the same entry in another collection · chain O against O, TM-score 1.00
- P00442 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (P00442) · a predicted model of the same protein · chain O against A, TM-score 0.98
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 P00442
- Elsewhere: RCSB PDB 2SOD · PDBe 2SOD · UniProt P00442
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