MolNFT v1 · #21546 · protein
Structure solution and molecular dynamics refinement of the yeast cu, zn enzyme superoxide dismutase
1SDY · COPPER,ZINC superoxide dismutase: “Structure solution and molecular dynamics refinement of the yeast cu, zn enzyme superoxide dismutase”. X-ray diffraction, 2 ligands (CU, ZN), 3 pockets (best druggability 0.72). MolNFT v1 #21546 on…
- 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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