Research workbench
Crystal structure of dyp-type peroxidase from cellulomonas bogoriensis
Analyse Crystal structure of dyp-type peroxidase from cellulomonas bogoriensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QZO
- Type
- protein
- Length
- 2,888 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxidase
- UniProt
- A0A0A0BZU2
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Peroxidase | protein | 361 | 27% helix, 21% strand | A0A0A0BZU2 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PGE · Triethylene glycol · additive · chains H
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 | 524 | 0.81 | 0.87 | 61 | HEM |
| 2 | 426 | 0.81 | 0.89 | 52 | HEM |
| 3 | 414 | 0.80 | 0.89 | 49 | HEM |
| 4 | 402 | 0.80 | 0.89 | 54 | HEM |
| 5 | 530 | 0.80 | 0.86 | 65 | HEM |
Interfaces
11 interfaces between chains.
- A–B · 2213 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2209 Ų buried · 42 hydrogen bonds · protein-protein
- G–H · 2188 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2187 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 698 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6QZO · Crystal structure of DyP-type peroxidase from Cellulomonas bogoriensis · 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 A0A0A0BZU2
- Elsewhere: RCSB PDB 6QZO · PDBe 6QZO · UniProt A0A0A0BZU2
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