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Structural basis for the catalytic activity of Thermomonospora curvata heme-containing DyP-type peroxidase.
Analyse Structural basis for the catalytic activity of Thermomonospora curvata… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JXU
- Type
- protein
- Length
- 720 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.751
- Source
- Thermomonospora curvata
- Molecule
- Dyp-type peroxidase family
- UniProt
- D1A807
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.751 · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dyp-type peroxidase family | protein | 360 | 28% helix, 23% strand | D1A807 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.84 | 0.92 | 59 | HEM |
| 2 | 425 | 0.84 | 0.91 | 55 | HEM |
| 3 | 390 | 0.76 | 0.86 | 44 | empty |
| 4 | 258 | 0.59 | 0.80 | 35 | empty |
| 5 | 246 | 0.59 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 2399 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 5JXU · Structural basis for the catalytic activity of thermomonospora curvata heme-containing… · 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
- Every structure of UniProt D1A807
- Elsewhere: RCSB PDB 5JXU · PDBe 5JXU · UniProt D1A807
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