Research workbench
Crystal structure of hepes bound dye decolorizing peroxidase from bacillus subtilis
Analyse Crystal structure of hepes bound dye decolorizing peroxidase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KMM
- Type
- protein
- Length
- 2,165 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DEFERROCHELATASE/PEROXIDASE efeb
- UniProt
- A0A4P9FDJ4
- Ligands
- HEM, NA, OXY, CL, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DEFERROCHELATASE/PEROXIDASE efeb | protein | 361 | 27% helix, 22% strand | A0A4P9FDJ4 |
| B, C | DEFERROCHELATASE/PEROXIDASE efeb | protein | 361 | 28% helix, 22% strand | A0A4P9FDJ4 |
| D | DEFERROCHELATASE/PEROXIDASE efeb | protein | 359 | 28% helix, 22% strand | A0A4P9FDJ4 |
| E | DEFERROCHELATASE/PEROXIDASE efeb | protein | 360 | 27% helix, 22% strand | A0A4P9FDJ4 |
| F | DEFERROCHELATASE/PEROXIDASE efeb | protein | 363 | 28% helix, 22% strand | A0A4P9FDJ4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · chains B, C
- OXY · Oxygen molecule · ion · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains C, D
- PO4 · Phosphate ion · ion · chains C
- GOL · Glycerol · additive · 6 copies · chains A, C, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, C, D, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.83 | 0.91 | 52 | HEM, OXY |
| 2 | 433 | 0.83 | 0.91 | 47 | HEM, OXY, GOL |
| 3 | 443 | 0.83 | 0.90 | 50 | HEM, OXY |
| 4 | 436 | 0.82 | 0.90 | 51 | HEM, OXY |
| 5 | 432 | 0.82 | 0.89 | 48 | HEM, OXY |
Interfaces
5 interfaces between chains.
- B–C · 2350 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 432 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 319 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 282 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 194 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KMM · Crystal Structure of HEPES bound 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 6KMM · PDBe 6KMM · UniProt A0A4P9FDJ4
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