Research workbench
Crystal structure of staphylococcus aureus response regulator arlr receiver domain in complex with BEF3 and mg
Analyse Crystal structure of staphylococcus aureus response regulator arlr receiver… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IS1
- Type
- protein
- Length
- 958 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator arlr
- UniProt
- Q2YY03
- Ligands
- BEF, MG
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Response regulator arlr | protein | 120 | 45% helix, 20% strand | Q2YY03 |
| C, D | Response regulator arlr | protein | 119 | 46% helix, 20% strand | Q2YY03 |
| B, F | Response regulator arlr | protein | 121 | 46% helix, 19% strand | Q2YY03 |
| E | Response regulator arlr | protein | 118 | 47% helix, 22% strand | Q2YY03 |
| G, H | Response regulator arlr | protein | 120 | 44% helix, 22% strand | Q2YY03 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 8 copies · chains A, C, B, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, C, B, D, E, F, G, H
- IMD · Imidazole · additive · 3 copies · chains B, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.57 | 0.90 | 10 | IMD |
| 2 | 165 | 0.55 | 0.81 | 22 | IMD |
| 3 | 269 | 0.54 | 0.76 | 27 | BEF, MG |
| 4 | 159 | 0.52 | 0.79 | 26 | empty |
| 5 | 190 | 0.52 | 0.77 | 35 | empty |
Interfaces
9 interfaces between chains.
- B–D · 1047 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 1027 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1018 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1009 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 485 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6IS1 · Crystal Structure of Staphylococcus aureus response regulator ArlR receiver domain in… · the same entry in another collection · chain H against H, TM-score 1.00
- Q2YY03 · AlphaFold monomer V2.0 prediction for response regulator arlr (Q2YY03) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 Q2YY03
- Elsewhere: RCSB PDB 6IS1 · PDBe 6IS1 · UniProt Q2YY03
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