Research workbench
Crystal structure of PBP3 transpeptidase domain from E. COLI in complex with AIC499
Analyse Crystal structure of PBP3 transpeptidase domain from E. COLI in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ONN
- Type
- protein
- Length
- 403 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
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 403 | 32% 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
- 12P · Dodecaethylene glycol · additive · 2 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 | 304 | 0.57 | 0.76 | 38 | VL5 |
| 2 | 56 | 0.27 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7ONN · Crystal structure of PBP3 transpeptidase domain 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 0.99
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 P0AD68
- Elsewhere: RCSB PDB 7ONN · PDBe 7ONN · UniProt P0AD68
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