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
- 3C1Q
- Type
- protein
- Length
- 231 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, NA, CL
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General secretion pathway protein F | protein | 115 | 71% helix, 0% strand | P45780 |
| B | General secretion pathway protein F | protein | 116 | 77% helix, 0% strand | P45780 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.69 | 0.85 | 34 | empty |
| 2 | 51 | 0.41 | 0.83 | 16 | empty |
| 3 | 80 | 0.40 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3C1Q · 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 3C1Q · PDBe 3C1Q · UniProt P45780
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.