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Structure of recombinant coprinus cinereus peroxidase determined to 2.0 a
Analyse Structure of recombinant coprinus cinereus peroxidase determined to 2.0 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H3J
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Coprinopsis cinerea
- Molecule
- Peroxidase
- EC
- 1.11.1.7
- UniProt
- P28314
- Ligands
- HEM, NAG, BMA, CA, MG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 43% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxidase (EC 1.11.1.7) | protein | 336 | 43% helix, 7% strand | P28314 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.80 | 0.89 | 39 | HEM |
| 2 | 380 | 0.79 | 0.88 | 40 | HEM |
| 3 | 127 | 0.36 | 0.73 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation, O-glycosylation).
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 P28314
- Elsewhere: RCSB PDB 1H3J · PDBe 1H3J · UniProt P28314
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