Research workbench
Arabidopsis thaliana peroxidase N
Analyse Arabidopsis thaliana peroxidase N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QGJ
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxidase N
- EC
- 1.11.1.-
- UniProt
- Q39034
- Ligands
- HEM, GSH, CA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxidase N (EC 1.11.1.-) | protein | 300 | 47% helix, 5% strand | Q39034 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- GSH · Glutathione · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.80 | 0.89 | 49 | HEM |
| 2 | 395 | 0.80 | 0.88 | 49 | HEM |
| 3 | 329 | 0.56 | 0.76 | 43 | empty |
| 4 | 191 | 0.47 | 0.75 | 31 | empty |
| 5 | 60 | 0.32 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
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 Q39034
- Elsewhere: RCSB PDB 1QGJ · PDBe 1QGJ · UniProt Q39034
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