MolNFT v1 · #113770 · protein
Controlled lid-opening in thermomyces lanuginosus lipase - a switch for activity and binding
5AP9: “Controlled lid-opening in thermomyces lanuginosus lipase - a switch for activity and binding”. X-ray diffraction, 2 ligands (NAG, SO4), 5 pockets (best druggability 0.51). MolNFT v1 #113770 on GenesisL1: 3D structure, binding sites…
- PDB
- 5AP9
- Type
- protein
- Length
- 527 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
- NAG, SO4
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase (EC 3.1.1.3) | protein | 269 | 32% helix, 24% strand | O59952 |
| B | Lipase (EC 3.1.1.3) | protein | 258 | 33% helix, 24% strand | O59952 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 227 | 0.51 | 0.76 | 35 | empty |
| 2 | 116 | 0.47 | 0.79 | 22 | empty |
| 3 | 128 | 0.47 | 0.78 | 19 | empty |
| 4 | 69 | 0.32 | 0.75 | 12 | empty |
| 5 | 68 | 0.30 | 0.74 | 17 | GOL |
Interfaces
1 interface between chains.
- A–B · 287 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5AP9 · Controlled lid-opening in Thermomyces lanuginosus lipase - a switch for activity and… · 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 0.98
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 5AP9 · PDBe 5AP9 · UniProt O59952
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