Research workbench
X-ray structure of a perdeuterated toho-1 R274N R276N double mutant beta-lactamase in complex with a fully deuterated boronic acid (bzb)
Analyse X-ray structure of a perdeuterated toho-1 R274N R276N double mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BD0
- Type
- protein
- Length
- 261 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase toho-1
- EC
- 3.5.2.6
- UniProt
- Q47066
- Ligands
- BZB, SO4
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase toho-1 (EC 3.5.2.6) | protein | 261 | 42% helix, 18% strand | Q47066 |
Ligands and binding sites
- BZB · Benzo[b]thiophene-2-boronic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.28 | 0.74 | 19 | BZB, SO4 |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4BD0 · X-ray structure of a perdeuterated Toho-1 R274N R276N double mutant Beta-lactamase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q47066 · AlphaFold monomer V2.0 prediction for beta-lactamase toho-1 (Q47066) · a predicted model of the same protein · chain A 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 Q47066
- Elsewhere: RCSB PDB 4BD0 · PDBe 4BD0 · UniProt Q47066
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