Research workbench
Crystal structure of the effector domain rid of vibrio vulnificus martx toxin
Analyse Crystal structure of the effector domain rid of vibrio vulnificus martx toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XN7
- Type
- protein
- Length
- 1,096 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative rtx-toxin
- UniProt
- F1CLG1
- Ligands
- CL, SO4
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative rtx-toxin | protein | 545 | 54% helix, 11% strand | F1CLG1 |
| B | Putative rtx-toxin | protein | 551 | 54% helix, 11% strand | F1CLG1 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.79 | 0.81 | 93 | empty |
| 2 | 728 | 0.69 | 0.76 | 55 | empty |
| 3 | 288 | 0.68 | 0.83 | 43 | empty |
| 4 | 135 | 0.68 | 0.89 | 25 | empty |
| 5 | 130 | 0.53 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1038 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5XN7 · Crystal structure of the effector domain RID of Vibrio vulnificus MARTX 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 F1CLG1
- Elsewhere: RCSB PDB 5XN7 · PDBe 5XN7 · UniProt F1CLG1
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