MolNFT v1 · #119440 · protein
Structure of thermobifida fusca dyp-type peroxidase and activity towards kraft lignin and lignin model compounds
5FW4 · Dye-decolorizing peroxidase TFU_3078: “Structure of thermobifida fusca dyp-type peroxidase and activity towards kraft lignin and lignin model…”. X-ray diffraction, 2 ligands (HEM, OXY), 8 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5FW4
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dye-decolorizing peroxidase TFU_3078
- EC
- 1.11.1.19
- UniProt
- Q47KB1
- Ligands
- HEM, OXY
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dye-decolorizing peroxidase TFU_3078 (EC 1.11.1.19) | protein | 368 | 35% helix, 22% strand | Q47KB1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.81 | 0.90 | 52 | HEM, OXY |
| 2 | 350 | 0.81 | 0.90 | 44 | HEM, OXY |
| 3 | 1158 | 0.77 | 0.79 | 112 | empty |
| 4 | 231 | 0.57 | 0.79 | 28 | empty |
| 5 | 219 | 0.55 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5FW4 · Structure of Thermobifida fusca DyP-type Peroxidase and Activity towards Kraft Lignin and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q47KB1 · AlphaFold monomer V2.0 prediction for dye-decolorizing peroxidase TFU_3078 (Q47KB1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q47KB1
- Elsewhere: RCSB PDB 5FW4 · PDBe 5FW4 · UniProt Q47KB1
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