MolNFT v1 · #40495 · protein
The structures of penicillium vitale catalase: resting state, oxidised state (compound I) and complex with aminotriazole
2IUF: “The structures of penicillium vitale catalase: resting state, oxidised state (compound I) and complex with…”. X-ray diffraction, 5 ligands (F50, HDD, NAG), 17 pockets (best druggability 0.85). MolNFT v1 #40495 on GenesisL1: 3D…
- PDB
- 2IUF
- Type
- protein
- Length
- 1,376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- Ligands
- F50, HDD, NAG, CA, O
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Catalase (EC 1.11.1.6) | protein | 688 | 32% helix, 16% strand | — |
Ligands and binding sites
- F50 · Ethaneperoxoic acid · ligand · 3 copies · chains A, E
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 2 copies · chains A, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains E, A
- CA · Calcium ion · metal · 6 copies · chains A, E
- O · Oxygen atom · ion · 2 copies · chains A, E
- ACT · Acetate ion · additive · 13 copies · chains A, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.85 | 0.91 | 111 | ACT, CA |
| 2 | 238 | 0.84 | 0.96 | 36 | HDD, O |
| 3 | 1054 | 0.84 | 0.85 | 111 | empty |
| 4 | 223 | 0.83 | 0.96 | 34 | HDD, O |
| 5 | 457 | 0.65 | 0.78 | 46 | empty |
Interfaces
1 interface between chains.
- A–E · 6366 Ų buried · 106 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 6 glycan (oxidation, N-glycosylation).
Compared structures
- 2IUF · The structures of Penicillium vitale catalase: resting state, oxidised state (compound I)… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 2IUF · PDBe 2IUF
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