Research workbench
Crystal structures of holo and cu-deficient CU/ZNSOD from the silkworm bombyx mori and the implications in amyotrophic lateral sclerosis
Analyse Crystal structures of holo and cu-deficient CU/ZNSOD from the silkworm bombyx… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L9Y
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [cu-zn]
- EC
- 1.15.1.1
- UniProt
- P82205
- Ligands
- ZN, CU
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 3% helix, 42% strand | P82205 |
| B | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 154 | 6% helix, 42% strand | P82205 |
Ligands and binding sites
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 | 57 | 0.55 | 0.89 | 20 | empty |
| 2 | 220 | 0.46 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 795 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3L9Y · Crystal structures of holo and Cu-deficient Cu/ZnSOD from the silkworm Bombyx mori and… · the same entry in another collection · chain A against A, TM-score 1.00
- P82205 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (P82205) · a predicted model of the same protein · chain B 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 P82205
- Elsewhere: RCSB PDB 3L9Y · PDBe 3L9Y · UniProt P82205
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