MolNFT v1 · #183985 · protein
Dictyostelium discoideum dye decolorizing peroxidase dypa in complex with cyanide.
7O9L: “Dictyostelium discoideum dye decolorizing peroxidase dypa in complex with cyanide.”. X-ray diffraction, 2 ligands (HEM, CYN), 8 pockets (best druggability 0.83). MolNFT v1 #183985 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7O9L
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dypa
- UniProt
- Q556V8
- Ligands
- HEM, CYN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dypa | protein | 306 | 34% helix, 25% strand | Q556V8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.83 | 0.92 | 44 | HEM, CYN |
| 2 | 338 | 0.81 | 0.91 | 42 | HEM, CYN |
| 3 | 290 | 0.64 | 0.81 | 24 | EDO |
| 4 | 144 | 0.46 | 0.77 | 19 | empty |
| 5 | 132 | 0.45 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1353 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7O9L · Dictyostelium discoideum dye decolorizing peroxidase DyPA 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 Q556V8
- Elsewhere: RCSB PDB 7O9L · PDBe 7O9L · UniProt Q556V8
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