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Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway
Analyse Crystal structure of the priming beta-ketosynthase from the R1128 polyketide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MZJ
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-ketoacylsynthase III
- EC
- 2.3.1.41
- UniProt
- Q9F6D4
- Ligands
- COA, ACE
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-ketoacylsynthase III (EC 2.3.1.41) | protein | 334 | 37% helix, 24% strand | Q9F6D4 |
| B | Beta-ketoacylsynthase III (EC 2.3.1.41) | protein | 334 | 34% helix, 24% strand | Q9F6D4 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.81 | 0.98 | 30 | empty |
| 2 | 198 | 0.68 | 0.85 | 31 | COA, ACE |
| 3 | 192 | 0.67 | 0.85 | 32 | COA, ACE |
| 4 | 147 | 0.63 | 0.86 | 42 | empty |
| 5 | 119 | 0.52 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3094 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1MZJ · Crystal Structure of the Priming beta-Ketosynthase from the R1128 Polyketide Biosynthetic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9F6D4 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 3… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9F6D4
- Elsewhere: RCSB PDB 1MZJ · PDBe 1MZJ · UniProt Q9F6D4
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