MolNFT v1 · #57831 · protein
Superoxide dismutase from aeropyrum pernix K1, apo-form
3AK1 · Superoxide dismutase [MN/FE]: “Superoxide dismutase from aeropyrum pernix K1, apo-form”. X-ray diffraction, 15 pockets (best druggability 0.84). MolNFT v1 #57831 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3AK1
- Type
- protein
- Length
- 850 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
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 212 | 53% helix, 13% strand | Q9Y8H8 |
| B, C | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 213 | 52% helix, 13% strand | Q9Y8H8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 26 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 | 257 | 0.84 | 0.96 | 37 | EDO |
| 2 | 57 | 0.74 | 0.99 | 17 | EDO |
| 3 | 58 | 0.69 | 0.96 | 18 | EDO |
| 4 | 55 | 0.67 | 0.95 | 18 | empty |
| 5 | 53 | 0.66 | 0.95 | 18 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 3038 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2980 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 940 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 291 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 3AK1 · PDBe 3AK1 · UniProt Q9Y8H8
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