MolNFT v1 · #90295 · protein
Crystal structure of a pheromone COB1 PRECURSOR/LIPOPROTEIN, yaec family (EF2496) from enterococcus faecalis V583 at 2.10 a resolution
4EF2 · Pheromone COB1/LIPOPROTEIN, yaec family: “Crystal structure of a pheromone COB1 PRECURSOR/LIPOPROTEIN, yaec family (EF2496) from enterococcus faecalis…”. X-ray diffraction, 2 ligands (MSE, CL), 3 pockets (best druggability 0.71).…
- PDB
- 4EF2
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pheromone COB1/LIPOPROTEIN, yaec family
- UniProt
- Q831K8
- Ligands
- MSE, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pheromone COB1/LIPOPROTEIN, yaec family | protein | 243 | 42% helix, 26% strand | Q831K8 |
| B | Pheromone COB1/LIPOPROTEIN, yaec family | protein | 241 | 42% helix, 26% strand | Q831K8 |
Ligands and binding sites
- MSE · Selenomethionine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A, B
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 | 711 | 0.71 | 0.77 | 59 | PGE, PE8 |
| 2 | 85 | 0.37 | 0.76 | 15 | empty |
| 3 | 57 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 459 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 4EF2 · Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from… · 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 Q831K8
- Elsewhere: RCSB PDB 4EF2 · PDBe 4EF2 · UniProt Q831K8
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