MolNFT v1 · #166925 · protein
Crystal structure of the diheme peroxidase btha Y463M variant from burkholderia thailandensis E264
6V59 · Di-haem cytochrome C peroxidase family protein: “Crystal structure of the diheme peroxidase btha Y463M variant from burkholderia thailandensis E264”. X-ray diffraction, 3 ligands (HEC, MG, CL), 9 pockets (best druggability 0.89).…
- PDB
- 6V59
- Type
- protein
- Length
- 838 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-haem cytochrome C peroxidase family protein
- UniProt
- Q2T6B0
- Ligands
- HEC, MG, CL
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Di-haem cytochrome C peroxidase family protein | protein | 419 | 39% helix, 9% strand | Q2T6B0 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 11 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.89 | 0.92 | 101 | HEC |
| 2 | 800 | 0.89 | 0.92 | 110 | HEC |
| 3 | 71 | 0.62 | 0.91 | 24 | CL |
| 4 | 291 | 0.54 | 0.75 | 39 | GOL |
| 5 | 242 | 0.54 | 0.77 | 42 | GOL |
Interfaces
1 interface between chains.
- A–B · 707 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 6V59 · Crystal structure of the diheme peroxidase BthA Y463M variant from Burkholderia… · 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 Q2T6B0
- Elsewhere: RCSB PDB 6V59 · PDBe 6V59 · UniProt Q2T6B0
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