Research workbench
Crystal structure of aimr from bacillus phage spbeta in complex with its signalling peptide
Analyse Crystal structure of aimr from bacillus phage spbeta in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y24
- Type
- protein
- Length
- 710 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aimr transcriptional regulator; Gly-met-pro-arg-gly-ala
- UniProt
- O64094
- Ligands
- BR
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aimr transcriptional regulator | protein | 348 | 73% helix, 0% strand | O64094 |
| C, D | Gly-met-pro-arg-gly-ala | protein | 6 | 0% helix, 0% strand | — |
| B | Aimr transcriptional regulator | protein | 350 | 73% helix, 0% strand | O64094 |
Ligands and binding sites
- BR · Bromide ion · ion · 5 copies · chains A, B
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 | 441 | 0.66 | 0.78 | 39 | empty |
| 2 | 385 | 0.65 | 0.79 | 41 | empty |
| 3 | 139 | 0.40 | 0.74 | 20 | empty |
| 4 | 106 | 0.37 | 0.74 | 19 | empty |
| 5 | 53 | 0.30 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 831 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 582 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 575 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 5Y24 · Crystal structure of AimR from Bacillus phage SPbeta in complex with its signalling… · 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 O64094
- Elsewhere: RCSB PDB 5Y24 · PDBe 5Y24 · UniProt O64094
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.