MolNFT v1 · #183984 · protein
Crystal structure of dyp-type peroxidase from dictyostelium discoideum in complex with an activated form of oxygen
7O9J · Dypa: “Crystal structure of dyp-type peroxidase from dictyostelium discoideum in complex with an activated form of…”. X-ray diffraction, 3 ligands (HEM, NA, OXY), 9 pockets (best druggability 0.83). MolNFT v1 #183984 on GenesisL1…
- PDB
- 7O9J
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dypa
- UniProt
- Q556V8
- Ligands
- HEM, NA, OXY
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dypa | protein | 306 | 33% helix, 25% strand | Q556V8 |
| B | Dypa | protein | 307 | 33% helix, 24% strand | Q556V8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.83 | 0.92 | 43 | HEM, OXY |
| 2 | 332 | 0.82 | 0.91 | 41 | HEM, OXY |
| 3 | 278 | 0.63 | 0.80 | 26 | EDO, NA |
| 4 | 136 | 0.45 | 0.77 | 17 | empty |
| 5 | 133 | 0.43 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1366 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7O9J · Crystal structure of DyP-type peroxidase from Dictyostelium discoideum in complex with an… · 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 7O9J · PDBe 7O9J · UniProt Q556V8
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