MolNFT v1 · #71703 · protein
Dye-decolorizing peroxidase (dyp) D171N
3MM1: “Dye-decolorizing peroxidase (dyp) D171N”. X-ray diffraction, 2 ligands (HEM, NAG), 3 pockets (best druggability 0.82). MolNFT v1 #71703 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MM1
- Type
- protein
- Length
- 439 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dyp
- EC
- 1.11.1.19
- UniProt
- Q8WZK8
- Ligands
- HEM, NAG
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dyp (EC 1.11.1.19) | protein | 439 | 31% helix, 20% strand | Q8WZK8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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 | 362 | 0.82 | 0.91 | 54 | HEM |
| 2 | 303 | 0.63 | 0.80 | 46 | empty |
| 3 | 73 | 0.38 | 0.78 | 20 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 3MM1 · Dye-decolorizing peroxidase (DyP) D171N · the same entry in another collection · chain A 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 Q8WZK8
- Elsewhere: RCSB PDB 3MM1 · PDBe 3MM1 · UniProt Q8WZK8
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