Research workbench
Cryo-EM structure of the encapsulated dyp-type peroxidase from mycobacterium smegmatis
Analyse Cryo-EM structure of the encapsulated dyp-type peroxidase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BOK
- Type
- protein
- Length
- 1,854 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dyp-type peroxidase
- EC
- 1.11.1.7
- UniProt
- I7GEX3
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Dyp-type peroxidase (EC 1.11.1.7) | protein | 309 | 28% helix, 23% strand | I7GEX3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
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 | 325 | 0.84 | 0.94 | 37 | HEM |
| 2 | 773 | 0.83 | 0.86 | 91 | HEM |
| 3 | 340 | 0.83 | 0.92 | 40 | HEM |
| 4 | 380 | 0.82 | 0.91 | 45 | HEM |
| 5 | 338 | 0.81 | 0.91 | 37 | HEM |
Interfaces
12 interfaces between chains.
- C–D · 1313 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1285 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1279 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 666 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 662 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7BOK · Cryo-EM structure of the encapsulated DyP-type peroxidase from Mycobacterium smegmatis · 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 I7GEX3
- Elsewhere: RCSB PDB 7BOK · PDBe 7BOK · UniProt I7GEX3
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