MolNFT v1 · #70063 · protein
Crystal structures of holo and cu-deficient CU/ZNSOD from the silkworm bombyx mori and the implications in amyotrophic lateral sclerosis
3L9E · Superoxide dismutase [cu-zn]: “Crystal structures of holo and cu-deficient CU/ZNSOD from the silkworm bombyx mori and the implications in…”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.68). MolNFT v1 #70063 on…
- PDB
- 3L9E
- Type
- protein
- Length
- 616 residues
- Chains
- 4
- 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
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 154 | 5% helix, 41% strand | P82205 |
Ligands and binding sites
- 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.68 | 0.93 | 29 | empty |
| 2 | 72 | 0.63 | 0.92 | 23 | empty |
| 3 | 267 | 0.49 | 0.73 | 35 | empty |
| 4 | 242 | 0.46 | 0.73 | 28 | empty |
| 5 | 230 | 0.45 | 0.73 | 38 | empty |
Interfaces
3 interfaces between chains.
- C–D · 780 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 767 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3L9E · 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 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 P82205
- Elsewhere: RCSB PDB 3L9E · PDBe 3L9E · UniProt P82205
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