Research workbench
Crystal structure of xanthomonas campestris olea E117D
Analyse Crystal structure of xanthomonas campestris olea E117D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VXH
- Type
- protein
- Length
- 671 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
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acp] synthase III (EC 2.3.1.41) | protein | 345 | 45% helix, 25% strand | Q8PDX2 |
| B | 3-oxoacyl-[acp] synthase III (EC 2.3.1.41) | protein | 326 | 46% helix, 24% strand | Q8PDX2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.80 | 0.88 | 72 | empty |
| 2 | 732 | 0.73 | 0.79 | 67 | empty |
| 3 | 220 | 0.63 | 0.83 | 38 | GOL |
| 4 | 202 | 0.59 | 0.81 | 33 | GOL |
Interfaces
1 interface between chains.
- A–B · 2183 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 5VXH · Crystal structure of Xanthomonas campestris OleA E117D · 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 5VXH · PDBe 5VXH · UniProt Q8PDX2
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