MolNFT v1 · #173252 · protein
Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (compound 4)
7ATX · Peptidoglycan D,D-transpeptidase ftsi: “Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (compound 4)”. X-ray diffraction, 1 ligand (S1B), 2 pockets (best druggability 0.56). MolNFT v1 #173252 on GenesisL1: 3D…
- PDB
- 7ATX
- Type
- protein
- Length
- 497 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
- S1B
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 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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