Research workbench
Crystal structure of the magnesium and beryllofluoride-activated vrar from staphylococcus aureus
Analyse Crystal structure of the magnesium and beryllofluoride-activated vrar from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IF4
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator protein vrar
- UniProt
- Q7A2Q1
- Ligands
- BEF, MG, SO4
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Response regulator protein vrar | protein | 208 | 54% helix, 15% strand | Q7A2Q1 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.61 | 0.92 | 14 | empty |
| 2 | 382 | 0.59 | 0.76 | 36 | empty |
| 3 | 113 | 0.51 | 0.81 | 29 | MG |
| 4 | 202 | 0.50 | 0.76 | 21 | empty |
| 5 | 111 | 0.50 | 0.81 | 30 | MG, BEF |
Interfaces
5 interfaces between chains.
- A–B · 1144 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 858 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 853 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 469 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 463 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4IF4 · Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7A2Q1 · AlphaFold monomer V2.0 prediction for response regulator protein vrar (Q7A2Q1) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 Q7A2Q1
- Elsewhere: RCSB PDB 4IF4 · PDBe 4IF4 · UniProt Q7A2Q1
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