Research workbench
Dyp-type peroxidase of auricularia auricula-judae (aaudypi) with meso- nitrated heme
Analyse Dyp-type peroxidase of auricularia auricula-judae (aaudypi) with meso- nitrated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AG1
- Type
- protein
- Length
- 891 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dye-decolorizing peroxidase
- EC
- 1.11.1.19
- UniProt
- I2DBY1
- Ligands
- N7H, NAG, NO2
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dye-decolorizing peroxidase (EC 1.11.1.19) | protein | 446 | 31% helix, 19% strand | I2DBY1 |
| B | Dye-decolorizing peroxidase (EC 1.11.1.19) | protein | 445 | 33% helix, 20% strand | I2DBY1 |
Ligands and binding sites
- N7H · Delta-meso nitroheme · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- NO2 · Nitrite ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.82 | 0.87 | 68 | N7H, NO2 |
| 2 | 635 | 0.82 | 0.86 | 67 | N7H, NO2 |
| 3 | 777 | 0.70 | 0.76 | 63 | GOL |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- I2DBY1 · AlphaFold monomer V2.0 prediction for dye-decolorizing peroxidase AAUDYP1 (I2DBY1) · a predicted model of the same protein · chain B 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 I2DBY1
- Elsewhere: RCSB PDB 5AG1 · PDBe 5AG1 · UniProt I2DBY1
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