MolNFT v1 · #135792 · protein
Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper-ion entry site
5U9M · Superoxide dismutase [cu-zn]: “Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper-ion entry site”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.76). MolNFT v1 #135792…
- PDB
- 5U9M
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [cu-zn]; Superoxide dismutase 1 copper chaperone
- EC
- 1.15.1.1
- UniProt
- P00441, P40202
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 7% helix, 39% strand | P00441 |
| B | Superoxide dismutase 1 copper chaperone | protein | 226 | 11% helix, 44% strand | P40202 |
| D | Superoxide dismutase 1 copper chaperone | protein | 234 | 13% helix, 46% strand | P40202 |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.76 | 0.80 | 86 | empty |
| 2 | 371 | 0.73 | 0.84 | 49 | empty |
| 3 | 72 | 0.49 | 0.84 | 14 | empty |
| 4 | 176 | 0.49 | 0.77 | 30 | empty |
| 5 | 153 | 0.45 | 0.76 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 963 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 962 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 214 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 107 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5U9M · Copper-Zinc Superoxide Dismutase is Activated through a Sulfenic Acid Intermediate at a… · the same entry in another collection · chain A against A, TM-score 1.00
- P40202 · AlphaFold monomer V2.0 prediction for superoxide dismutase 1 copper chaperone (P40202) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P00441
- Every structure of UniProt P40202
- Elsewhere: RCSB PDB 5U9M · PDBe 5U9M · UniProt P00441 · UniProt P40202
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.