MolNFT v1 · #82781 · protein

Dye-decolorizing peroxidase (dyp) complex with 2,6-dimethoxyphenol

3VXJ: “Dye-decolorizing peroxidase (dyp) complex with 2,6-dimethoxyphenol”. X-ray diffraction, 3 ligands (3DM, HEM, NAG), 3 pockets (best druggability 0.82). MolNFT v1 #82781 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VXJ
Type: protein
Length: 438 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: 3DM, 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	438	31% helix, 20% strand	Q8WZK8

Ligands and binding sites

3DM · 2,6-dimethoxyphenol · ligand · 2 copies · chains A
HEM · Protoporphyrin IX containing Fe · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
DMS · Dimethyl sulfoxide · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	364	0.82	0.91	52	HEM, 3DM
2	322	0.65	0.81	42	empty
3	80	0.39	0.78	21	DMS

Modifications

Observed in the structure: 1 glycan (N-glycosylation).

Compared structures

3VXJ · Dye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol · 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 3VXJ · PDBe 3VXJ · UniProt Q8WZK8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.