Research workbench
Crystal structure of the diheme peroxidase btha Y463M variant from burkholderia thailandensis E264
Analyse Crystal structure of the diheme peroxidase btha Y463M variant from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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