Research workbench
Superoxide dismutase from aeropyrum pernix K1, mn-bound form
Analyse Superoxide dismutase from aeropyrum pernix K1, mn-bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AK2
- Type
- protein
- Length
- 839 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
- MN
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 211 | 52% helix, 13% strand | Q9Y8H8 |
| B | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 209 | 53% helix, 13% strand | Q9Y8H8 |
| C | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 210 | 53% helix, 13% strand | Q9Y8H8 |
| D | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 209 | 53% helix, 13% strand | Q9Y8H8 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.84 | 0.96 | 36 | EDO |
| 2 | 56 | 0.68 | 0.96 | 18 | empty |
| 3 | 58 | 0.68 | 0.95 | 18 | empty |
| 4 | 276 | 0.61 | 0.80 | 31 | EDO |
| 5 | 279 | 0.59 | 0.78 | 31 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 2840 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2802 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 963 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 962 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 290 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3AK2 · Superoxide dismutase from Aeropyrum pernix K1, Mn-bound form · the same entry in another collection · chain D against D, 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 3AK2 · PDBe 3AK2 · UniProt Q9Y8H8
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