MolNFT v1 · #137727 · protein
Crystal structure of xanthomonas campestris olea E117A bound with cerulenin
5VXE · 3-oxoacyl-[acp] synthase III: “Crystal structure of xanthomonas campestris olea E117A bound with cerulenin”. X-ray diffraction, 2 ligands (CER, MN), 2 pockets (best druggability 0.68). MolNFT v1 #137727 on GenesisL1: 3D structure…
- PDB
- 5VXE
- Type
- protein
- Length
- 332 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acp] synthase III
- UniProt
- Q8PDX2
- Ligands
- CER, MN
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acp] synthase III | protein | 332 | 47% helix, 23% strand | Q8PDX2 |
Ligands and binding sites
- CER · (2S, 3R)-3-hydroxy-4-oxo-7,10-trans,trans-dodecadienamide · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.68 | 0.79 | 52 | CER |
| 2 | 62 | 0.27 | 0.72 | 12 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5VXE · Crystal structure of Xanthomonas campestris OleA E117A bound with Cerulenin · 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 0.97
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 5VXE · PDBe 5VXE · UniProt Q8PDX2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.