Research workbench

Dye-decolorizing peroxidase (dyp) at 1.4 a resolution

Analyse Dye-decolorizing peroxidase (dyp) at 1.4 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AFV
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 0.81

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dyp (EC 1.11.1.19)	protein	439	32% 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	354	0.81	0.91	51	HEM
2	329	0.64	0.80	43	empty
3	85	0.39	0.77	21	empty

Modifications

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

Compared structures

3AFV · Dye-decolorizing peroxidase (DyP) at 1.4 A resolution · 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 3AFV · PDBe 3AFV · UniProt Q8WZK8

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