Research workbench
Crystal structure of veratryl alcohol bound dye decolorizing peroxidase from bacillus subtilis
Analyse Crystal structure of veratryl alcohol bound dye decolorizing peroxidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DLK
- Type
- protein
- Length
- 2,170 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DEFERROCHELATASE/PEROXIDASE
- EC
- 1.11.1.-
- UniProt
- A0A6G2J275
- Ligands
- HEM, VOH, CL, OXY, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 363 | 27% helix, 22% strand | A0A6G2J275 |
| B | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 361 | 27% helix, 22% strand | A0A6G2J275 |
| D | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 361 | 27% helix, 22% strand | A0A6G2J275 |
| E | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 362 | 26% helix, 23% strand | A0A6G2J275 |
| F | DEFERROCHELATASE/PEROXIDASE (EC 1.11.1.-) | protein | 360 | 26% helix, 21% strand | A0A6G2J275 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- VOH · Veratryl alcohol · ligand · 2 copies · chains C, E
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F
- OXY · Oxygen molecule · ion · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 13 copies · chains A, E, D, B, C, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, E, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.84 | 0.91 | 53 | HEM, OXY |
| 2 | 454 | 0.84 | 0.91 | 52 | HEM, OXY, GOL |
| 3 | 467 | 0.83 | 0.90 | 51 | HEM, OXY, GOL |
| 4 | 426 | 0.83 | 0.90 | 50 | HEM, OXY, GOL |
| 5 | 435 | 0.81 | 0.89 | 50 | HEM, OXY, CL |
Interfaces
7 interfaces between chains.
- A–E · 2361 Ų buried · 41 hydrogen bonds · protein-protein
- B–E · 659 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 407 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 347 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 292 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7DLK · Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus… · 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 7DLK · PDBe 7DLK · UniProt A0A6G2J275
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