Research workbench
Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 4)
Analyse Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ATX
- Type
- protein
- Length
- 497 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.795
- Source
- Pseudomonas aeruginosa
- Molecule
- Peptidoglycan D,D-transpeptidase FtsI
- EC
- 3.4.16.4
- UniProt
- G3XD46
- Ligands
- S1B
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · resolution 1.795 · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase FtsI (EC 3.4.16.4) | protein | 497 | 34% helix, 27% strand | G3XD46 |
Ligands and binding sites
- S1B · 4-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborole-6-carbonyl)-1,3,3-trimethylpiperazin-2-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.56 | 0.75 | 47 | empty |
| 2 | 163 | 0.43 | 0.74 | 26 | S1B |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7ATX · Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (compound 4) · the same entry in another collection · chain A against A, TM-score 1.00
- G3XD46 · AlphaFold monomer V2.0 prediction for peptidoglycan D,D-transpeptidase ftsi (G3XD46) · 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 G3XD46
- Elsewhere: RCSB PDB 7ATX · PDBe 7ATX · UniProt G3XD46
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