Research workbench
Structure solution and molecular dynamics refinement of the yeast cu, zn enzyme superoxide dismutase
Analyse Structure solution and molecular dynamics refinement of the yeast cu, zn enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SDY
- Type
- protein
- Length
- 612 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
- P00445
- Ligands
- CU, ZN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | COPPER,ZINC superoxide dismutase (EC 1.15.1.1) | protein | 153 | 5% helix, 37% strand | P00445 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.72 | 0.76 | 96 | empty |
| 2 | 259 | 0.67 | 0.84 | 36 | empty |
| 3 | 252 | 0.64 | 0.82 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 647 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 636 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 352 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 240 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1SDY · Structure solution and molecular dynamics refinement of the yeast CU,ZN enzyme superoxide… · the same entry in another collection · chain A against A, TM-score 1.00
- P00445 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (P00445) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00445
- Elsewhere: RCSB PDB 1SDY · PDBe 1SDY · UniProt P00445
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