Research workbench
Crystal Structure of the adhesin domain of Epf from Streptococcus pyogenes in P212121
Analyse Crystal Structure of the adhesin domain of Epf from Streptococcus pyogenes in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ES8
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.58
- Source
- Streptococcus pyogenes
- Molecule
- Epf
- Ligands
- NA, K
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.58 · 2 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epf | protein | 302 | 5% helix, 47% strand | — |
| B | Epf | protein | 297 | 5% helix, 47% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- K · Potassium ion · metal · chains B
- ACT · Acetate ion · additive · 2 copies · chains A
- GOL · Glycerol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.66 | 0.77 | 65 | NA |
| 2 | 494 | 0.62 | 0.75 | 44 | empty |
| 3 | 93 | 0.37 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 608 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4ES8 · Crystal structure of the adhesin domain of epf from streptococcus pyogenes in P212121 · 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
- Elsewhere: RCSB PDB 4ES8 · PDBe 4ES8
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