Research workbench
Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (compound 3)
Analyse Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (compound 3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ATW
- Type
- protein
- Length
- 493 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan D,D-transpeptidase ftsi
- EC
- 3.4.16.4
- UniProt
- G3XD46
- Ligands
- RZZ
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 493 | 35% helix, 27% strand | G3XD46 |
Ligands and binding sites
- RZZ · 1-Hydroxy-1,3-dihydro-2,1-benzoxaborole-6-carboxylic acid · ligand · chains A
- GOL · Glycerol · additive · 3 copies · 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 | 289 | 0.55 | 0.76 | 36 | empty |
| 2 | 118 | 0.38 | 0.75 | 25 | RZZ |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7ATW · Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 3) · 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 7ATW · PDBe 7ATW · UniProt G3XD46
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