Research workbench
Crystal structure of a decolorizing peroxidase (dyp) from auricularia auricula-judae
Analyse Crystal structure of a decolorizing peroxidase (dyp) from auricularia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W7J
- Type
- protein
- Length
- 1,783 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dye-decolorizing peroxidase
- EC
- 1.11.1.19
- UniProt
- I2DBY1
- Ligands
- HEM
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dye-decolorizing peroxidase (EC 1.11.1.19) | protein | 445 | 31% helix, 20% strand | I2DBY1 |
| B | Dye-decolorizing peroxidase (EC 1.11.1.19) | protein | 447 | 32% helix, 20% strand | I2DBY1 |
| D | Dye-decolorizing peroxidase (EC 1.11.1.19) | protein | 446 | 31% helix, 19% strand | I2DBY1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.85 | 0.95 | 44 | HEM |
| 2 | 337 | 0.85 | 0.94 | 45 | HEM |
| 3 | 634 | 0.82 | 0.87 | 76 | HEM |
| 4 | 662 | 0.81 | 0.86 | 69 | HEM |
| 5 | 867 | 0.81 | 0.83 | 68 | empty |
Interfaces
6 interfaces between chains.
- A–C · 733 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 673 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 422 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 270 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4W7J · Crystal structure of a decolorizing peroxidase (dyp) from auricularia auricula-judae · the same entry in another collection · chain D against D, TM-score 1.00
- I2DBY1 · AlphaFold monomer V2.0 prediction for dye-decolorizing peroxidase AAUDYP1 (I2DBY1) · a predicted model of the same protein · chain C 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 4W7J · PDBe 4W7J · UniProt I2DBY1
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