Research workbench
Crystal structure of the complex of three phase partition treated lipase from thermomyces lanuginosa with lauric acid and P- nitrobenzaldehyde (pnb) at 2.1 resolution
Analyse Crystal 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
- 4KJX
- 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
- DAO, XXH, NAG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipase (EC 3.1.1.3) | protein | 269 | 32% helix, 23% strand | O59952 |
Ligands and binding sites
- DAO · Lauric acid · ligand · 2 copies · chains A, B
- XXH · 4-nitrobenzaldehyde · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- EDO · 1,2-ethanediol · additive · 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 | 244 | 0.58 | 0.79 | 40 | GOL, EDO |
| 2 | 95 | 0.41 | 0.78 | 21 | empty |
| 3 | 104 | 0.38 | 0.75 | 22 | DAO |
| 4 | 88 | 0.36 | 0.75 | 19 | ACT, DAO |
Interfaces
1 interface between chains.
- A–B · 577 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4KJX · Crystal 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 4KJX · PDBe 4KJX · UniProt O59952
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