MolNFT v1 · #114461 · protein
Crystal structure of the istb aaa+ domain bound to ADP-BEF3
5BQ5 · Insertion sequence IS5376 putative ATP-binding protein: “Crystal structure of the istb aaa+ domain bound to ADP-BEF3”. X-ray diffraction, 3 ligands (ADP, BEF, MG), 4 pockets (best druggability 0.70). MolNFT v1 #114461 on GenesisL1…
- PDB
- 5BQ5
- Type
- protein
- Length
- 547 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insertion sequence IS5376 putative ATP-binding protein
- UniProt
- Q45619
- Ligands
- ADP, BEF, MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Insertion sequence IS5376 putative ATP-binding protein | protein | 180 | 51% helix, 15% strand | Q45619 |
| B | Insertion sequence IS5376 putative ATP-binding protein | protein | 187 | 50% helix, 15% strand | Q45619 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.70 | 0.79 | 64 | ADP, MG, BEF |
| 2 | 159 | 0.54 | 0.80 | 31 | empty |
| 3 | 172 | 0.54 | 0.80 | 31 | ADP, MG, BEF |
| 4 | 132 | 0.49 | 0.79 | 27 | ADP, MG, BEF |
Interfaces
2 interfaces between chains.
- B–C · 873 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 5BQ5 · Crystal structure of the IstB AAA+ domain bound to ADP-BeF3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q45619 · AlphaFold monomer V2.0 prediction for insertion sequence IS5376 putative ATP-binding… · a predicted model of the same protein · 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 Q45619
- Elsewhere: RCSB PDB 5BQ5 · PDBe 5BQ5 · UniProt Q45619
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