Research workbench
Crystal structure of PBP3 from E. COLI in complex with AIC499
Analyse Crystal structure of PBP3 from E. COLI 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
- 7ONW
- Type
- protein
- Length
- 485 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
- P0AD68
- Ligands
- VL5, PO4
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 485 | 34% helix, 21% strand | P0AD68 |
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 · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.58 | 0.87 | 24 | empty |
| 2 | 291 | 0.54 | 0.75 | 36 | VL5 |
| 3 | 72 | 0.48 | 0.83 | 21 | empty |
| 4 | 86 | 0.41 | 0.78 | 22 | empty |
| 5 | 74 | 0.38 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7ONW · Crystal structure of PBP3 from E. coli in complex with AIC499 · the same entry in another collection · chain A against A, TM-score 1.00
- P0AD68 · AlphaFold monomer V2.0 prediction for peptidoglycan D,D-transpeptidase ftsi (P0AD68) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P0AD68
- Elsewhere: RCSB PDB 7ONW · PDBe 7ONW · UniProt P0AD68
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