MolNFT v1 · #137726 · protein
Crystal structure of xanthomonas campestris olea E117A
5VXD · 3-oxoacyl-[acp] synthase III: “Crystal structure of xanthomonas campestris olea E117A”. X-ray diffraction, 6 pockets (best druggability 0.83). MolNFT v1 #137726 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VXD
- Type
- protein
- Length
- 685 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acp] synthase III
- EC
- 2.3.1.41
- UniProt
- Q8PDX2
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acp] synthase III (EC 2.3.1.41) | protein | 345 | 44% helix, 25% strand | Q8PDX2 |
| B | 3-oxoacyl-[acp] synthase III (EC 2.3.1.41) | protein | 340 | 43% helix, 25% strand | Q8PDX2 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.83 | 0.91 | 56 | empty |
| 2 | 486 | 0.81 | 0.88 | 51 | empty |
| 3 | 180 | 0.62 | 0.83 | 37 | GOL |
| 4 | 196 | 0.61 | 0.82 | 31 | GOL |
| 5 | 83 | 0.37 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2356 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 5VXD · Crystal structure of Xanthomonas campestris OleA E117A · 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 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 Q8PDX2
- Elsewhere: RCSB PDB 5VXD · PDBe 5VXD · UniProt Q8PDX2
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