MolNFT v1 · #154797 · protein
Crystal structure of dye decolorizing peroxidase from bacillus subtilis
6KMN · DEFERROCHELATASE/PEROXIDASE efeb: “Crystal structure of dye decolorizing peroxidase from bacillus subtilis”. X-ray diffraction, 3 ligands (HEM, OXY, CL), 20 pockets (best druggability 0.83). MolNFT v1 #154797 on GenesisL1: 3D…
- PDB
- 6KMN
- Type
- protein
- Length
- 1,449 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DEFERROCHELATASE/PEROXIDASE efeb
- UniProt
- A0A4P9FDJ4
- Ligands
- HEM, OXY, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DEFERROCHELATASE/PEROXIDASE efeb | protein | 361 | 27% helix, 22% strand | A0A4P9FDJ4 |
| B, D | DEFERROCHELATASE/PEROXIDASE efeb | protein | 363 | 26% helix, 22% strand | A0A4P9FDJ4 |
| C | DEFERROCHELATASE/PEROXIDASE efeb | protein | 362 | 27% helix, 22% strand | A0A4P9FDJ4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · 2 copies · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.83 | 0.91 | 48 | HEM, OXY |
| 2 | 402 | 0.83 | 0.91 | 51 | HEM, OXY |
| 3 | 396 | 0.83 | 0.91 | 47 | HEM, OXY |
| 4 | 408 | 0.81 | 0.89 | 49 | HEM, OXY, GOL |
| 5 | 383 | 0.71 | 0.83 | 55 | CL |
Interfaces
4 interfaces between chains.
- B–D · 2581 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2491 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 278 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KMN · Crystal Structure of Dye Decolorizing peroxidase from Bacillus subtilis · 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 A0A4P9FDJ4
- Elsewhere: RCSB PDB 6KMN · PDBe 6KMN · UniProt A0A4P9FDJ4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.