MolNFT v1 · #12553 · protein
Crystal structure of aspergillus fumigatus mnsod
1KKC · Manganese superoxide dismutase: “Crystal structure of aspergillus fumigatus mnsod”. X-ray diffraction, 1 ligand (MN), 15 pockets (best druggability 0.57). MolNFT v1 #12553 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1KKC
- Type
- protein
- Length
- 799 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- Q92450
- Ligands
- MN
- Pockets
- 15 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, Y | Manganese superoxide dismutase (EC 1.15.1.1) | protein | 200 | 58% helix, 13% strand | Q92450 |
| B | Manganese superoxide dismutase (EC 1.15.1.1) | protein | 199 | 58% helix, 13% strand | Q92450 |
| X | Manganese superoxide dismutase (EC 1.15.1.1) | protein | 200 | 58% helix, 13% strand | Q92450 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.57 | 0.82 | 26 | empty |
| 2 | 132 | 0.57 | 0.83 | 23 | empty |
| 3 | 124 | 0.55 | 0.83 | 25 | empty |
| 4 | 104 | 0.55 | 0.84 | 21 | empty |
| 5 | 244 | 0.48 | 0.74 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–B · 953 Ų buried · 20 hydrogen bonds · protein-protein
- X–Y · 943 Ų buried · 20 hydrogen bonds · protein-protein
- A–X · 831 Ų buried · 2 hydrogen bonds · protein-protein
- B–Y · 795 Ų buried · 3 hydrogen bonds · protein-protein
- B–X · 162 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1KKC · Crystal structure of Aspergillus fumigatus MnSOD · the same entry in another collection · chain A against A, TM-score 1.00
- Q92450 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn], mitochondrial (Q92450) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q92450
- Elsewhere: RCSB PDB 1KKC · PDBe 1KKC · UniProt Q92450
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