MolNFT v1 · #151716 · protein
Room temperature structure of lipase from T. lanuginosa at 2.5 a resolution in chipx microfluidic device
6HW1: “Room temperature structure of lipase from T. lanuginosa at 2.5 a resolution in chipx microfluidic device”. X-ray diffraction, 3 ligands (NAG, MG, PO4), 4 pockets (best druggability 0.58). MolNFT v1 #151716 on GenesisL1: 3D…
- PDB
- 6HW1
- 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
- NAG, MG, PO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipase (EC 3.1.1.3) | protein | 269 | 33% helix, 25% strand | O59952 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
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 | 234 | 0.58 | 0.79 | 40 | empty |
| 2 | 100 | 0.40 | 0.77 | 21 | empty |
| 3 | 97 | 0.36 | 0.75 | 20 | empty |
| 4 | 83 | 0.36 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6HW1 · Room temperature structure of lipase from T. lanuginosa at 2.5 a resolution in chipx… · 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 6HW1 · PDBe 6HW1 · UniProt O59952
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