MolNFT v1 · #75067 · protein
Crystal structure of the lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with ethylferulate
3PFB: “Crystal structure of the lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with…”. X-ray diffraction, 3 ligands (ZYC, NH4, CL), 7 pockets (best druggability 0.79). MolNFT v1 #75067 on GenesisL1: 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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