Research workbench
Crystal structure of LAE6 SER161ALA mutant, an ALPHA/BETA hydrolase enzyme from the metagenome of lake arreo, spain
Analyse Crystal structure of LAE6 SER161ALA mutant, an ALPHA/BETA hydrolase enzyme from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JD4
- Type
- protein
- Length
- 2,536 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LAE6
- Ligands
- BEN, SO4, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | LAE6 | protein | 317 | 42% helix, 18% strand | — |
Ligands and binding sites
- BEN · Benzamidine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 10 copies · chains A, H, B, E, C, F, D, G
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G
- GOL · Glycerol · additive · 27 copies · chains A, B, C, D, E, G, F, H
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 3 copies · chains A, B, H, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.84 | 0.85 | 101 | BEN |
| 2 | 1004 | 0.84 | 0.85 | 107 | BEN, SO4 |
| 3 | 953 | 0.84 | 0.85 | 94 | PE3, GOL, BEN |
| 4 | 671 | 0.83 | 0.87 | 68 | BEN |
| 5 | 623 | 0.82 | 0.87 | 63 | BEN |
Interfaces
10 interfaces between chains.
- B–E · 1066 Ų buried · 15 hydrogen bonds · protein-protein
- D–G · 1064 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1049 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 1047 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 550 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5JD4 · Crystal structure of LAE6 Ser161Ala mutant, an alpha/beta hydrolase enzyme from the… · 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
- Elsewhere: RCSB PDB 5JD4 · PDBe 5JD4
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