MolNFT v1 · #154546 · protein
Wildtype E53, a microbial hsl esterase
6KEU · Lipase: “Wildtype E53, a microbial hsl esterase”. X-ray diffraction, 3 ligands (D8F, 6NA, SO4), 7 pockets (best druggability 0.81). MolNFT v1 #154546 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KEU
- Type
- protein
- Length
- 1,236 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- UniProt
- A0A074MDU6
- Ligands
- D8F, 6NA, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lipase | protein | 309 | 39% helix, 17% strand | A0A074MDU6 |
Ligands and binding sites
- D8F · (4-nitrophenyl) hexanoate · ligand · 4 copies · chains A, B, C, D
- 6NA · Hexanoic acid · ligand · chains C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.81 | 0.84 | 87 | D8F |
| 2 | 848 | 0.79 | 0.82 | 84 | D8F |
| 3 | 478 | 0.76 | 0.84 | 54 | D8F, EDO |
| 4 | 454 | 0.75 | 0.84 | 57 | D8F |
| 5 | 76 | 0.34 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 920 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 898 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 633 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6KEU · Wildtype E53, a microbial HSL esterase · 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 A0A074MDU6
- Elsewhere: RCSB PDB 6KEU · PDBe 6KEU · UniProt A0A074MDU6
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