Research workbench
Changes in crystallographic structure and thermostability of a CU,ZN superoxide dismutase mutant resulting from the removal of buried cysteine
Analyse Changes in crystallographic structure and thermostability of a CU,ZN superoxide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SOD
- 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 0.62
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, Y, G, B | COPPER,ZINC superoxide dismutase (EC 1.15.1.1) | protein | 151 | 6% helix, 42% strand | P00442 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains O, Y, G, B
- CU · Copper (II) ion · metal · 4 copies · chains O, Y, G, B
- ZN · Zinc ion · metal · 4 copies · chains O, Y, G, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.62 | 0.78 | 50 | empty |
| 2 | 259 | 0.56 | 0.77 | 33 | empty |
| 3 | 59 | 0.30 | 0.75 | 23 | empty |
Interfaces
2 interfaces between chains.
- O–Y · 359 Ų buried · 0 hydrogen bonds · protein-protein
- G–B · 315 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 3SOD · Changes in crystallographic structure and thermostability of a CU,ZN superoxide dismutase… · 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 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 P00442
- Elsewhere: RCSB PDB 3SOD · PDBe 3SOD · UniProt P00442
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