MolNFT v1 · #38384 · protein

Crystal structure of a dye-decolorizing peroxidase (dyp) from bacteroides thetaiotaomicron vpi-5482 at 1.6 a resolution

2GVK · Heme peroxidase: “Crystal structure of a dye-decolorizing peroxidase (dyp) from bacteroides thetaiotaomicron vpi-5482 at 1.6 a…”. X-ray diffraction, 3 ligands (UNL, NA, CL), 1 pocket (best druggability 0.73). MolNFT v1 #38384 on…

PDB: 2GVK
Type: protein
Length: 309 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heme peroxidase
Ligands: UNL, NA, CL
Pockets: 1 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heme peroxidase	protein	309	31% helix, 26% strand	—

Ligands and binding sites

UNL · Unknown ligand · ligand · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 5 copies · chains A
ACY · Acetic acid · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	201	0.73	0.89	40	EDO, ACY

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

2GVK · Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides… · 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
Elsewhere: RCSB PDB 2GVK · PDBe 2GVK

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