Research workbench
Crystal structure of LIP2 lipase from yarrowia lipolytica at 1.7 a resolution
Analyse Crystal structure of LIP2 lipase from yarrowia lipolytica at 1.7 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O0D
- Type
- protein
- Length
- 2,095 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triacylglycerol lipase
- EC
- 3.1.1.3
- UniProt
- Q9P8F7
- Ligands
- NAG, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Triacylglycerol lipase (EC 3.1.1.3) | protein | 301 | 34% helix, 23% strand | Q9P8F7 |
| D | Triacylglycerol lipase (EC 3.1.1.3) | protein | 297 | 34% helix, 23% strand | Q9P8F7 |
| F | Triacylglycerol lipase (EC 3.1.1.3) | protein | 298 | 35% helix, 23% strand | Q9P8F7 |
| G | Triacylglycerol lipase (EC 3.1.1.3) | protein | 296 | 33% helix, 23% strand | Q9P8F7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D, E, G, F
- K · Potassium ion · metal · 7 copies · chains A, B, C, D, E, F, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 13 copies · chains A, B, C, D, E, F
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.85 | 0.86 | 120 | MPD |
| 2 | 551 | 0.79 | 0.86 | 69 | MPD |
| 3 | 575 | 0.79 | 0.85 | 57 | MRD |
| 4 | 877 | 0.73 | 0.77 | 68 | MPD |
| 5 | 923 | 0.71 | 0.76 | 72 | MPD |
Interfaces
11 interfaces between chains.
- B–E · 739 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 690 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 658 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 633 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 473 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 3O0D · Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9P8F7
- Elsewhere: RCSB PDB 3O0D · PDBe 3O0D · UniProt Q9P8F7
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