MolNFT v1 · #11378 · protein
Crystal structure of manganese catalase from lactobacillus plantarum complexed with azide
1JKV · Pseudocatalase: “Crystal structure of manganese catalase from lactobacillus plantarum complexed with azide”. X-ray diffraction, 4 ligands (MN3, CA, OH), 13 pockets (best druggability 0.89). MolNFT v1 #11378 on GenesisL1: 3D…
- PDB
- 1JKV
- Type
- protein
- Length
- 1,596 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudocatalase
- EC
- 1.11.1.6
- UniProt
- P60355
- Ligands
- MN3, CA, OH, AZI
- Pockets
- 13 · best druggability 0.89
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 | Pseudocatalase (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
- OH · Hydroxide ion · ion · 18 copies · chains A, B, C, D, E, F
- AZI · Azide ion · ion · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, F, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.89 | 0.90 | 193 | EDO |
| 2 | 240 | 0.64 | 0.82 | 36 | empty |
| 3 | 250 | 0.63 | 0.81 | 33 | empty |
| 4 | 260 | 0.62 | 0.80 | 35 | empty |
| 5 | 230 | 0.62 | 0.81 | 33 | empty |
Interfaces
15 interfaces between chains.
- A–F · 5070 Ų buried · 106 hydrogen bonds · protein-protein
- D–E · 5023 Ų buried · 104 hydrogen bonds · protein-protein
- B–C · 5022 Ų buried · 106 hydrogen bonds · protein-protein
- A–B · 1711 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 1710 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1JKV · Crystal Structure of Manganese Catalase from Lactobacillus plantarum complexed with azide · 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 1JKV · PDBe 1JKV · UniProt P60355
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