MolNFT v1 · #57833 · protein
Superoxide dismutase from aeropyrum pernix K1, fe-bound form
3AK3 · Superoxide dismutase [MN/FE]: “Superoxide dismutase from aeropyrum pernix K1, fe-bound form”. X-ray diffraction, 1 ligand (FE), 14 pockets (best druggability 0.84). MolNFT v1 #57833 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3AK3
- Type
- protein
- Length
- 843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [MN/FE]
- EC
- 1.15.1.1
- UniProt
- Q9Y8H8
- Ligands
- FE
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 210 | 52% helix, 13% strand | Q9Y8H8 |
| B | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 213 | 52% helix, 13% strand | Q9Y8H8 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.84 | 0.96 | 34 | EDO |
| 2 | 58 | 0.75 | 1.00 | 18 | empty |
| 3 | 54 | 0.69 | 0.97 | 18 | empty |
| 4 | 50 | 0.69 | 0.97 | 18 | empty |
| 5 | 50 | 0.66 | 0.96 | 16 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 2976 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2826 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 963 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 961 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 280 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3AK3 · Superoxide dismutase from Aeropyrum pernix K1, Fe-bound form · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y8H8 · AlphaFold monomer V2.0 prediction for superoxide dismutase [MN/FE] (Q9Y8H8) · 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 Q9Y8H8
- Elsewhere: RCSB PDB 3AK3 · PDBe 3AK3 · UniProt Q9Y8H8
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