MolNFT v1 · #100811 · protein
Crystal structure of the ternary complex of lipase from thermomyces lanuginosa with ethylacetoacetate and P-nitrobenzaldehyde at 2.3 a resolution
4N8S: “Crystal structure of the ternary complex of lipase from thermomyces lanuginosa with ethylacetoacetate and…”. X-ray diffraction, 3 ligands (XXH, EAC, NAG), 5 pockets (best druggability 0.57). MolNFT v1 #100811 on GenesisL1: 3D…
- PDB
- 4N8S
- 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
- XXH, EAC, NAG
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipase (EC 3.1.1.3) | protein | 269 | 33% helix, 26% strand | O59952 |
Ligands and binding sites
- XXH · 4-nitrobenzaldehyde · ligand · 2 copies · chains A, B
- EAC · ethyl 3-oxobutanoate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.57 | 0.79 | 40 | XXH, GOL |
| 2 | 117 | 0.39 | 0.75 | 21 | empty |
| 3 | 57 | 0.37 | 0.80 | 17 | empty |
| 4 | 68 | 0.35 | 0.77 | 18 | EAC |
| 5 | 68 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 593 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4N8S · Crystal Structure of the ternary complex of lipase from Thermomyces lanuginosa with… · 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 4N8S · PDBe 4N8S · UniProt O59952
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