Research workbench
Selenomethionine variant of Tannerella forsythia promirolysin mutant E225A
Analyse Selenomethionine variant of Tannerella forsythia promirolysin mutant E225A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R7U
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Tannerella forsythia
- Molecule
- Mirolysin
- UniProt
- A0A0F7IPS1
- Ligands
- CA, ZN, BO3
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.6 · 2 distinct chains · 30% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mirolysin | protein | 307 | 29% helix, 17% strand | A0A0F7IPS1 |
| B | Mirolysin | protein | 308 | 31% helix, 15% strand | A0A0F7IPS1 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- BO3 · Boric acid · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.68 | 0.75 | 80 | empty |
| 2 | 104 | 0.49 | 0.81 | 18 | empty |
| 3 | 90 | 0.44 | 0.79 | 19 | empty |
| 4 | 118 | 0.42 | 0.76 | 19 | empty |
| 5 | 107 | 0.38 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 295 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified, 4 disulfide (engineered, disulfide, oxidation).
Compared structures
- 6R7U · Selenomethionine variant of tannerella forsythia promirolysin mutant E225A · 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 A0A0F7IPS1
- Elsewhere: RCSB PDB 6R7U · PDBe 6R7U · UniProt A0A0F7IPS1
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