MolNFT v1 · #86032 · protein
Crystal structure of a fungal dyp-type peroxidase from auricularia auricula-judae
4AU9 · Dyp-type peroxidase I: “Crystal structure of a fungal dyp-type peroxidase from auricularia auricula-judae”. X-ray diffraction, 4 ligands (HEM, TAM, NAG), 3 pockets (best druggability 0.82). MolNFT v1 #86032 on GenesisL1: 3D…
- PDB
- 4AU9
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dyp-type peroxidase I
- EC
- 1.11.1.19
- Ligands
- HEM, TAM, NAG, BMA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dyp-type peroxidase I (EC 1.11.1.19) | protein | 448 | 29% helix, 20% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 6 copies · chains A, B
- ACT · Acetate ion · 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 | 633 | 0.82 | 0.86 | 72 | HEM, GOL |
| 2 | 618 | 0.82 | 0.86 | 64 | HEM, GOL |
| 3 | 791 | 0.70 | 0.76 | 65 | GOL |
Interfaces
1 interface between chains.
- A–B · 652 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 4AU9 · Crystal Structure of a Fungal DyP-Type Peroxidase from Auricularia auricula-judae · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 4AU9 · PDBe 4AU9
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