Research workbench
The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae
Analyse The three-dimensional structure of the cytoplasmic domains of EpsF from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VMA
- Type
- protein
- Length
- 234 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- VIBRIO CHOLERAE
- Molecule
- General secretion pathway protein F
- UniProt
- P45780
- Ligands
- CA, IOD
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General secretion pathway protein F | protein | 122 | 72% helix, 0% strand | P45780 |
| B | General secretion pathway protein F | protein | 112 | 77% helix, 0% strand | P45780 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.71 | 0.90 | 28 | empty |
| 2 | 91 | 0.42 | 0.78 | 17 | IOD |
| 3 | 52 | 0.40 | 0.82 | 17 | empty |
| 4 | 67 | 0.35 | 0.77 | 17 | IOD |
Interfaces
1 interface between chains.
- A–B · 979 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2VMA · The three-dimensional structure of the cytoplasmic domains of epsf from the type 2… · the same entry in another collection · chain A against A, TM-score 1.00
- P45780 · AlphaFold monomer V2.0 prediction for type II secretion system protein F (P45780) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P45780
- Elsewhere: RCSB PDB 2VMA · PDBe 2VMA · UniProt P45780
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