MolNFT v1 · #116488 · protein
Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with cefoperazone
5DF8 · Cell division protein: “Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with cefoperazone”. X-ray diffraction, 2 ligands (59F, CL), 7 pockets (best druggability 0.79). MolNFT v1 #116488 on…
- PDB
- 5DF8
- Type
- protein
- Length
- 1,003 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
- 59F, CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein (EC 2.4.1.129) | protein | 514 | 35% helix, 26% strand | Q51504 |
| B | Cell division protein (EC 2.4.1.129) | protein | 489 | 36% helix, 23% strand | Q51504 |
Ligands and binding sites
- 59F · (2R,4R,5R)-2-[(1R)-1-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}-2-oxoethyl]-5-methyl-1,3-thiazinane-4-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.79 | 0.81 | 86 | GOL, CL |
| 2 | 835 | 0.76 | 0.80 | 65 | 59F |
| 3 | 365 | 0.61 | 0.77 | 37 | 59F |
| 4 | 442 | 0.61 | 0.75 | 44 | empty |
| 5 | 190 | 0.47 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1290 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5DF8 · 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 5DF8 · PDBe 5DF8 · UniProt Q51504
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