Research workbench
Crystal structure of the lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with caffeic acid
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
- 3S2Z
- Type
- protein
- Length
- 501 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
- DHC, CL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cinnamoyl esterase (EC 3.1.1.-) | protein | 251 | 35% helix, 28% strand | D3YEX6 |
| B | Cinnamoyl esterase (EC 3.1.1.-) | protein | 250 | 34% helix, 29% strand | D3YEX6 |
Ligands and binding sites
- DHC · Caffeic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 16 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 | 118 | 0.78 | 0.96 | 21 | empty |
| 2 | 178 | 0.58 | 0.81 | 31 | empty |
| 3 | 140 | 0.55 | 0.82 | 29 | CL |
| 4 | 113 | 0.54 | 0.82 | 28 | DHC |
| 5 | 111 | 0.52 | 0.82 | 31 | DHC |
Interfaces
1 interface between chains.
- A–B · 1216 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3S2Z · 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 3S2Z · PDBe 3S2Z · UniProt D3YEX6
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