Research workbench
Crystal Structure of Gram Negative Toxin
Analyse Crystal Structure of Gram Negative Toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NAL
- Type
- protein
- Length
- 947 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Desulfobulbus propionicus (strain ATCC 33891 / DSM 2032 / 1pr3)
- Molecule
- Thiol-activated cytolysin
- UniProt
- E8RGW2
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 21% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiol-activated cytolysin | protein | 474 | 22% helix, 43% strand | E8RGW2 |
| B | Thiol-activated cytolysin | protein | 473 | 20% helix, 42% strand | E8RGW2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.67 | 0.79 | 58 | empty |
| 2 | 237 | 0.61 | 0.81 | 39 | empty |
| 3 | 299 | 0.61 | 0.79 | 43 | IMD |
| 4 | 270 | 0.59 | 0.79 | 36 | IMD |
| 5 | 343 | 0.57 | 0.76 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 6NAL · Crystal structure of gram negative toxin · 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 E8RGW2
- Elsewhere: RCSB PDB 6NAL · PDBe 6NAL · UniProt E8RGW2
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