Research workbench
Structure of P. aeruginosa PBP3 in complex with an aryl boronic acid (compound 2)
Analyse Structure of P. aeruginosa PBP3 in complex with an aryl boronic acid (compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ATO
- Type
- protein
- Length
- 503 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
- RXW
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 503 | 34% helix, 25% strand | G3XD46 |
Ligands and binding sites
- RXW · (5-methyl-1H-indazol-6-yl)boronic acid · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.65 | 0.81 | 42 | RXW, DMS |
| 2 | 404 | 0.59 | 0.75 | 50 | empty |
| 3 | 59 | 0.34 | 0.77 | 12 | empty |
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7ATO · Structure of P. aeruginosa PBP3 in complex with an aryl boronic acid (Compound 2) · 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 0.98
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 7ATO · PDBe 7ATO · UniProt G3XD46
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