MolNFT v1 · #97941 · protein
Crystal structure of C143S xanthomonas campestris olea bound with myristic acid and myrisotoyl-CoA
4KU3 · 3-oxoacyl-[acp] synthase III: “Crystal structure of C143S xanthomonas campestris olea bound with myristic acid and myrisotoyl-CoA”. X-ray diffraction, 2 ligands (MYR, MYA), 4 pockets (best druggability 0.85). MolNFT v1 #97941 on…
- PDB
- 4KU3
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acp] synthase III
- UniProt
- Q8PDX2
- Ligands
- MYR, MYA
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acp] synthase III | protein | 339 | 45% helix, 26% strand | Q8PDX2 |
| B | 3-oxoacyl-[acp] synthase III | protein | 337 | 45% helix, 26% strand | Q8PDX2 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains B
- MYA · Tetradecanoyl-coa · ligand · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.85 | 0.90 | 59 | MYR, MYA |
| 2 | 482 | 0.76 | 0.84 | 63 | PEG |
| 3 | 171 | 0.57 | 0.81 | 28 | empty |
| 4 | 141 | 0.44 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2366 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 4KU3 · Crystal Structure of C143S Xanthomonas Campestris OleA bound with myristic acid and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PDX2 · AlphaFold monomer V2.0 prediction for acyl-COA:ACYL-CoA alkyltransferase (Q8PDX2) · a predicted model of the same protein · chain A 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 Q8PDX2
- Elsewhere: RCSB PDB 4KU3 · PDBe 4KU3 · UniProt Q8PDX2
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