Research workbench
Dictyostelium discoideum dye decolorizing peroxidase dypa in complex with an activated form of oxygen and veratryl alcohol
Analyse Dictyostelium discoideum dye decolorizing peroxidase dypa in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ODZ
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dypa
- UniProt
- Q556V8
- Ligands
- VOH, HEM, OXY
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dypa | protein | 307 | 34% helix, 24% strand | Q556V8 |
Ligands and binding sites
- VOH · Veratryl alcohol · ligand · 4 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.83 | 0.93 | 43 | HEM, OXY |
| 2 | 332 | 0.82 | 0.92 | 45 | HEM, OXY |
| 3 | 263 | 0.62 | 0.80 | 24 | EDO |
| 4 | 161 | 0.47 | 0.76 | 20 | VOH |
| 5 | 142 | 0.46 | 0.77 | 18 | VOH |
Interfaces
1 interface between chains.
- A–B · 1396 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7ODZ · Dictyostelium discoideum dye decolorizing peroxidase DyPA in complex with an activated… · 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 Q556V8
- Elsewhere: RCSB PDB 7ODZ · PDBe 7ODZ · UniProt Q556V8
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