MolNFT v1 · #116487 · protein
Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with azlocillin
5DF7 · Cell division protein: “Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with azlocillin”. X-ray diffraction, 2 ligands (59H, CL), 5 pockets (best druggability 0.81). MolNFT v1 #116487 on…
- PDB
- 5DF7
- Type
- protein
- Length
- 1,005 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein
- EC
- 2.4.1.129
- UniProt
- Q51504
- Ligands
- 59H, CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein (EC 2.4.1.129) | protein | 515 | 34% helix, 26% strand | Q51504 |
| B | Cell division protein (EC 2.4.1.129) | protein | 490 | 36% helix, 23% strand | Q51504 |
Ligands and binding sites
- 59H · (2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-{[(2R)-2-{[(2-oxoimidazolidin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}ethyl]-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.81 | 0.83 | 87 | GOL |
| 2 | 1060 | 0.78 | 0.80 | 100 | 59H, CL |
| 3 | 364 | 0.62 | 0.78 | 38 | 59H |
| 4 | 227 | 0.49 | 0.75 | 30 | empty |
| 5 | 62 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1278 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5DF7 · Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex… · 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 5DF7 · PDBe 5DF7 · UniProt Q51504
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