Research workbench
Crystal structure of ethyl acetoacetate treated lipase from thermomyces lanuginosa at 2.9 a resolution
Analyse Crystal structure of ethyl acetoacetate treated lipase from thermomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GBG
- 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
- EAC, NAG
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipase (EC 3.1.1.3) | protein | 269 | 31% helix, 25% strand | O59952 |
Ligands and binding sites
- EAC · ethyl 3-oxobutanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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 | 224 | 0.56 | 0.78 | 36 | empty |
| 2 | 106 | 0.40 | 0.76 | 20 | empty |
| 3 | 101 | 0.37 | 0.75 | 21 | empty |
| 4 | 67 | 0.33 | 0.76 | 16 | empty |
| 5 | 59 | 0.33 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 561 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4GBG · Crystal structure of Ethyl acetoacetate treated lipase from Thermomyces lanuginosa at 2.9… · 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 4GBG · PDBe 4GBG · UniProt O59952
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