MolNFT v1 · #16794 · protein
Crystal structure of the Y42F mutant of manganese catalase from lactobacillus plantarum at 1.33A resolution
1O9I: “Crystal structure of the Y42F mutant of manganese catalase from lactobacillus plantarum at 1.33A resolution”. X-ray diffraction, 4 ligands (MN3, CA, NA), 9 pockets (best druggability 0.88). MolNFT v1 #16794 on GenesisL1: 3D…
- PDB
- 1O9I
- Type
- protein
- Length
- 1,596 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese catalase
- EC
- 1.11.1.6
- UniProt
- P60355
- Ligands
- MN3, CA, NA, O
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Manganese catalase (EC 1.11.1.6) | protein | 266 | 53% helix, 6% strand | P60355 |
Ligands and binding sites
- MN3 · Manganese (III) ion · metal · 12 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, F, B, C, D, E
- NA · Sodium ion · metal · 2 copies · chains A, F, D, E
- O · Oxygen atom · ion · 6 copies · chains A, B, C, D, E, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 5 copies · chains A, D, F, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.88 | 0.90 | 150 | empty |
| 2 | 223 | 0.62 | 0.82 | 37 | empty |
| 3 | 66 | 0.62 | 0.92 | 18 | empty |
| 4 | 244 | 0.61 | 0.80 | 36 | empty |
| 5 | 216 | 0.60 | 0.81 | 37 | empty |
Interfaces
15 interfaces between chains.
- A–F · 5008 Ų buried · 104 hydrogen bonds · protein-protein
- B–C · 4971 Ų buried · 104 hydrogen bonds · protein-protein
- D–E · 4942 Ų buried · 105 hydrogen bonds · protein-protein
- C–E · 1742 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1735 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 1O9I · Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum… · the same entry in another collection · chain C against C, TM-score 1.00
- P60355 · AlphaFold monomer V2.0 prediction for manganese catalase (P60355) · 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 P60355
- Elsewhere: RCSB PDB 1O9I · PDBe 1O9I · UniProt P60355
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