Research workbench
Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides thetaiotaomicron VPI-5482 at 1.6 A resolution
Analyse Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GVK
- Type
- protein
- Length
- 309 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Bacteroides thetaiotaomicron
- Molecule
- Heme peroxidase
- Ligands
- UNL, NA, CL
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.6 · 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.
| Volume (ų) | 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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