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The structure of Thermomyces Lanuginosa lipase in complex with 1,3 diacylglycerol in a monoclinic crystal form
Analyse The structure of Thermomyces Lanuginosa lipase in complex with 1,3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O9F
- Type
- protein
- Length
- 1,614 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.48
- Source
- Thermomyces lanuginosus
- Molecule
- Lipase
- EC
- 3.1.1.3
- UniProt
- O59952
- Ligands
- OCA, LTV, NAG, CA, PO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.48 · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, D, F | Lipase (EC 3.1.1.3) | protein | 269 | 33% helix, 24% strand | O59952 |
Ligands and binding sites
- OCA · Octanoic acid (caprylic acid) · ligand · 6 copies · chains A, D, B, E, C, F
- LTV · 2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate · ligand · 6 copies · chains A, D, F, B, C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, E, D, F
- CA · Calcium ion · metal · 8 copies · chains A, B, C, E, D, F
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.81 | 0.82 | 90 | OCA, LTV |
| 2 | 1188 | 0.79 | 0.80 | 91 | OCA, LTV |
| 3 | 167 | 0.56 | 0.81 | 33 | empty |
| 4 | 183 | 0.55 | 0.80 | 29 | empty |
| 5 | 186 | 0.55 | 0.80 | 29 | empty |
Interfaces
7 interfaces between chains.
- A–F · 509 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 494 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 481 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 480 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 7 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- O59952 · AlphaFold monomer V2.0 prediction for lipase (O59952) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O59952
- Elsewhere: RCSB PDB 6O9F · PDBe 6O9F · UniProt O59952
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