MolNFT v1 · #117059 · protein
Structural and functional characterization of pqsbc, a condensing enzyme in the biosynthesis of the pseudomonas aeruginosa quinolone signal
5DWZ · 3-oxoacyl-[acyl-carrier-protein] synthase 3: “Structural and functional characterization of pqsbc, a condensing enzyme in the biosynthesis of the…”. X-ray diffraction, 3 ligands (NA, PO4, CL), 20 pockets (best druggability 0.87).…
- PDB
- 5DWZ
- Type
- protein
- Length
- 2,474 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3; 3-oxoacyl-(acyl carrier protein) synthase III
- EC
- 2.3.1.180
- UniProt
- A0A0C6EZ24, A0A072ZZD2
- Ligands
- NA, PO4, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 340 | 32% helix, 28% strand | A0A0C6EZ24 |
| B, A | 3-oxoacyl-(acyl carrier protein) synthase III | protein | 278 | 25% helix, 29% strand | A0A072ZZD2 |
| D | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 340 | 32% helix, 28% strand | A0A0C6EZ24 |
| F | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 340 | 32% helix, 27% strand | A0A0C6EZ24 |
| E | 3-oxoacyl-(acyl carrier protein) synthase III | protein | 279 | 25% helix, 28% strand | A0A072ZZD2 |
| H | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 341 | 32% helix, 27% strand | A0A0C6EZ24 |
| G | 3-oxoacyl-(acyl carrier protein) synthase III | protein | 278 | 25% helix, 29% strand | A0A072ZZD2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains E
- PO4 · Phosphate ion · ion · 20 copies · chains C, F, D, H, A, E
- CL · Chloride ion · ion · 2 copies · chains C, B, D, A
- GOL · Glycerol · additive · 7 copies · chains C, B, D, A
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 4 copies · chains C, F, D, H
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains D, H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C, F
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.87 | 0.90 | 101 | PO4, MPO |
| 2 | 539 | 0.84 | 0.89 | 73 | PO4, MPO |
| 3 | 445 | 0.83 | 0.90 | 64 | PO4 |
| 4 | 263 | 0.54 | 0.76 | 37 | CL |
| 5 | 208 | 0.51 | 0.76 | 28 | empty |
Interfaces
8 interfaces between chains.
- F–E · 2343 Ų buried · 34 hydrogen bonds · protein-protein
- D–A · 2330 Ų buried · 34 hydrogen bonds · protein-protein
- C–B · 2303 Ų buried · 30 hydrogen bonds · protein-protein
- H–G · 2303 Ų buried · 36 hydrogen bonds · protein-protein
- D–H · 989 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5DWZ · Structural and functional characterization of PqsBC, a condensing enzyme in the… · the same entry in another collection · chain C against C, 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 A0A0C6EZ24
- Every structure of UniProt A0A072ZZD2
- Elsewhere: RCSB PDB 5DWZ · PDBe 5DWZ · UniProt A0A0C6EZ24 · UniProt A0A072ZZD2
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