MolNFT v1 · #140168 · protein
Crystal structure of aimr from bacillus phage spbeta in complex with its signalling peptide
5Y24 · Aimr transcriptional regulator: “Crystal structure of aimr from bacillus phage spbeta in complex with its signalling peptide”. X-ray diffraction, 1 ligand (BR), 5 pockets (best druggability 0.66). MolNFT v1 #140168 on GenesisL1: 3D…
- 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
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