MolNFT v1 · #184356 · protein
Crystal structure of PBP3 transpeptidase domain from E. COLI in complex with AIC499
7ONN · Peptidoglycan D,D-transpeptidase ftsi: “Crystal structure of PBP3 transpeptidase domain from E. COLI in complex with AIC499”. X-ray diffraction, 1 ligand (VL5), 2 pockets (best druggability 0.57). MolNFT v1 #184356 on GenesisL1: 3D…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.