Research workbench
Crystal structure of the lactobacillus johnsonii cinnamoyl esterase LJ0536
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
- 3PF8
- Type
- protein
- Length
- 495 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
- NA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cinnamoyl esterase (EC 3.1.1.-) | protein | 251 | 33% helix, 27% strand | D3YEX6 |
| B | Cinnamoyl esterase (EC 3.1.1.-) | protein | 244 | 34% helix, 30% strand | D3YEX6 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.77 | 0.95 | 21 | NA |
| 2 | 181 | 0.58 | 0.81 | 33 | empty |
| 3 | 119 | 0.54 | 0.83 | 28 | empty |
| 4 | 124 | 0.50 | 0.80 | 31 | empty |
| 5 | 102 | 0.48 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1277 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3PF8 · Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 · 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 3PF8 · PDBe 3PF8 · UniProt D3YEX6
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