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Crystal structure of dye decolorizing peroxidase from bacillus subtilis at acidic pH
Analyse Crystal structure of dye decolorizing peroxidase from bacillus subtilis at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E5Q
- Type
- protein
- Length
- 707 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DEFERROCHELATASE/PEROXIDASE
- EC
- 1.11.1.-
- UniProt
- A0A6G2J275
- Ligands
- HEM, NA, CL, OXY
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 355 | 28% helix, 24% strand | A0A6G2J275 |
| B | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 352 | 28% helix, 23% strand | A0A6G2J275 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.82 | 0.90 | 44 | HEM, OXY, EDO |
| 2 | 473 | 0.80 | 0.87 | 48 | HEM, OXY, EDO, GOL, NA, CL |
| 3 | 120 | 0.64 | 0.87 | 27 | EDO, CL |
| 4 | 364 | 0.59 | 0.76 | 42 | PEG, CL, NA |
| 5 | 121 | 0.59 | 0.85 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2354 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 7E5Q · Crystal Structure of Dye Decolorizing peroxidase from Bacillus subtilis at acidic pH · 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 A0A6G2J275
- Elsewhere: RCSB PDB 7E5Q · PDBe 7E5Q · UniProt A0A6G2J275
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