Research workbench
Crystal structure of PBP3 from P. aeruginosa in complex with AIC499
Analyse Crystal structure of PBP3 from P. aeruginosa in complex with AIC499 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ONK
- Type
- protein
- Length
- 1,017 residues
- Chains
- 2
- 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
- VL5, CL
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 512 | 34% helix, 25% strand | G3XD46 |
| B | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 505 | 35% helix, 26% strand | G3XD46 |
Ligands and binding sites
- VL5 · (2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.71 | 0.76 | 77 | GOL |
| 2 | 364 | 0.64 | 0.79 | 50 | empty |
| 3 | 363 | 0.62 | 0.78 | 39 | VL5, CL, GOL |
| 4 | 409 | 0.61 | 0.77 | 42 | VL5 |
| 5 | 197 | 0.45 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 790 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7ONK · Crystal structure of PBP3 from P. aeruginosa in complex with AIC499 · 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 0.95
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 7ONK · PDBe 7ONK · UniProt G3XD46
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