MolNFT v1 · #28314 · protein
X-ray structure of a bacterial COPPER,ZINC superoxide dismutase
1YAI · Copper, zinc superoxide dismutase: “X-ray structure of a bacterial COPPER,ZINC superoxide dismutase”. X-ray diffraction, 2 ligands (CU, ZN), 2 pockets (best druggability 0.57). MolNFT v1 #28314 on GenesisL1: 3D structure, binding…
- PDB
- 1YAI
- Type
- protein
- Length
- 452 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper, zinc superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P00446
- Ligands
- CU, ZN
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Copper, zinc superoxide dismutase (EC 1.15.1.1) | protein | 151 | 7% helix, 38% strand | P00446 |
| C | Copper, zinc superoxide dismutase (EC 1.15.1.1) | protein | 150 | 7% helix, 39% strand | P00446 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.57 | 0.77 | 38 | empty |
| 2 | 222 | 0.48 | 0.75 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 345 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 325 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1YAI · X-ray structure of a bacterial COPPER,ZINC superoxide dismutase · the same entry in another collection · chain A against A, TM-score 1.00
- P00446 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (P00446) · a predicted model of the same protein · chain C 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 P00446
- Elsewhere: RCSB PDB 1YAI · PDBe 1YAI · UniProt P00446
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