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Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from burkholderia xenovorans
Analyse Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DFE
- Type
- protein
- Length
- 1,291 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3
- EC
- 2.3.1.180
- UniProt
- Q13VL5
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 322 | 39% helix, 29% strand | Q13VL5 |
| B | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 324 | 39% helix, 29% strand | Q13VL5 |
| D | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 323 | 39% helix, 29% strand | Q13VL5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.81 | 0.98 | 35 | empty |
| 2 | 134 | 0.80 | 0.98 | 33 | empty |
| 3 | 675 | 0.71 | 0.78 | 83 | empty |
| 4 | 127 | 0.68 | 0.90 | 33 | empty |
| 5 | 118 | 0.67 | 0.89 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2623 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 2548 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 262 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 4DFE · Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia… · 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 Q13VL5
- Elsewhere: RCSB PDB 4DFE · PDBe 4DFE · UniProt Q13VL5
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