Research workbench
Crystal structure of the beryllofluoride-activated liar from enterococcus faecium
Analyse Crystal structure of the beryllofluoride-activated liar from enterococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HEV
- Type
- protein
- Length
- 837 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator protein vrar
- UniProt
- S4FAU8
- Ligands
- BEF, MG
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Response regulator protein vrar | protein | 208 | 50% helix, 13% strand | S4FAU8 |
| F, C | Response regulator protein vrar | protein | 210 | 52% helix, 13% strand | S4FAU8 |
| B | Response regulator protein vrar | protein | 209 | 53% helix, 13% strand | S4FAU8 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 4 copies · chains A, F, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, F, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.56 | 0.77 | 33 | empty |
| 2 | 241 | 0.51 | 0.75 | 23 | empty |
| 3 | 92 | 0.46 | 0.81 | 25 | BEF |
| 4 | 73 | 0.35 | 0.76 | 16 | BEF |
| 5 | 53 | 0.32 | 0.77 | 17 | BEF |
Interfaces
3 interfaces between chains.
- F–B · 1010 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 776 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 748 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5HEV · Crystal Structure of the beryllofluoride-activated LiaR from Enterococcus faecium · the same entry in another collection · chain B against B, 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 S4FAU8
- Elsewhere: RCSB PDB 5HEV · PDBe 5HEV · UniProt S4FAU8
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