Research workbench
Crystal structure of the Y42F mutant of manganese catalase from lactobacillus plantarum at 1.33A resolution
Analyse Crystal structure of the Y42F mutant of manganese catalase from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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