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Dye-decolorizing peroxidase (dyp) in complex with cyanide

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

PDB: 3MM2
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, CYN
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
CYN · Cyanide ion · ion · 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	372	0.82	0.91	53	HEM, CYN
2	326	0.64	0.80	49	empty
3	61	0.36	0.79	19	empty

Modifications

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

Compared structures

3MM2 · Dye-decolorizing peroxidase (DyP) in complex with cyanide · 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 3MM2 · PDBe 3MM2 · UniProt Q8WZK8

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