MolNFT v1 · #139687 · protein
Crystal structure of the effector domain rid of vibrio vulnificus martx toxin
5XN7 · Putative rtx-toxin: “Crystal structure of the effector domain rid of vibrio vulnificus martx toxin”. X-ray diffraction, 2 ligands (CL, SO4), 15 pockets (best druggability 0.79). MolNFT v1 #139687 on GenesisL1: 3D structure, binding…
- 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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