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
- 2VMB
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General secretion pathway protein F
- UniProt
- P45780
- Ligands
- CA
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General secretion pathway protein F | protein | 121 | 74% helix, 0% strand | P45780 |
| B | General secretion pathway protein F | protein | 115 | 78% helix, 0% strand | P45780 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.72 | 0.87 | 40 | empty |
| 2 | 87 | 0.39 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 869 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2VMB · 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 0.99
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 2VMB · PDBe 2VMB · UniProt P45780
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