Research workbench
Structure of the complex of three phase partition treated lipase from thermomyces lanuginosa with 16-hydroxypalmitic acid at 2.4 a resolution
Analyse Structure of the complex of three phase partition treated lipase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GI1
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- EC
- 3.1.1.3
- UniProt
- O59952
- Ligands
- 16Y
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipase (EC 3.1.1.3) | protein | 269 | 34% helix, 25% strand | O59952 |
Ligands and binding sites
- 16Y · 16-hydroxyhexadecanoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.58 | 0.79 | 40 | empty |
| 2 | 58 | 0.43 | 0.82 | 14 | empty |
| 3 | 107 | 0.41 | 0.76 | 20 | 16Y |
| 4 | 102 | 0.37 | 0.75 | 21 | 16Y |
Interfaces
1 interface between chains.
- A–B · 599 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4GI1 · Structure of the complex of three phase partition treated lipase from Thermomyces… · the same entry in another collection · chain A against A, TM-score 1.00
- O59952 · AlphaFold monomer V2.0 prediction for lipase (O59952) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 4GI1 · PDBe 4GI1 · UniProt O59952
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