Research workbench
Crystal structure of the lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with ethylferulate
Analyse Crystal structure of the lactobacillus johnsonii cinnamoyl esterase LJ0536… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PFB
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cinnamoyl esterase
- EC
- 3.1.1.-
- UniProt
- D3YEX6
- Ligands
- ZYC, NH4, CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cinnamoyl esterase (EC 3.1.1.-) | protein | 250 | 35% helix, 28% strand | D3YEX6 |
Ligands and binding sites
- ZYC · ethyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 16 copies · chains A, B
- CL · Chloride ion · ion · 4 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 | 122 | 0.79 | 0.96 | 20 | empty |
| 2 | 124 | 0.60 | 0.85 | 29 | NH4, ZYC |
| 3 | 216 | 0.58 | 0.80 | 34 | NH4 |
| 4 | 162 | 0.55 | 0.81 | 30 | CL |
| 5 | 100 | 0.54 | 0.83 | 28 | ZYC |
Interfaces
1 interface between chains.
- A–B · 1197 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3PFB · Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant… · the same entry in another collection · chain A against A, TM-score 1.00
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 D3YEX6
- Elsewhere: RCSB PDB 3PFB · PDBe 3PFB · UniProt D3YEX6
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