MolNFT v1 · #151899 · protein
Crystal structure of pseudomonas aeruginosa penicillin-binding protein 3 in complex with amoxicillin
6I1E · Peptidoglycan D,D-transpeptidase ftsi: “Crystal structure of pseudomonas aeruginosa penicillin-binding protein 3 in complex with amoxicillin”. X-ray diffraction, 1 ligand (AXL), 5 pockets (best druggability 0.62). MolNFT v1 #151899…
- PDB
- 6I1E
- Type
- protein
- Length
- 515 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
- Q51504
- Ligands
- AXL
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 515 | 34% helix, 24% strand | Q51504 |
Ligands and binding sites
- AXL · 2-{1-[2-amino-2-(4-hydroxy-phenyl)-acetylamino]-2-oxo-ethyl}-5,5-dimethyl-thiazolidine-4-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.62 | 0.79 | 39 | AXL |
| 2 | 236 | 0.55 | 0.78 | 39 | empty |
| 3 | 71 | 0.46 | 0.82 | 19 | empty |
| 4 | 104 | 0.45 | 0.79 | 21 | empty |
| 5 | 114 | 0.41 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6I1E · Crystal structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q51504
- Elsewhere: RCSB PDB 6I1E · PDBe 6I1E · UniProt Q51504
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