Research workbench
Crystal structure of dog gastric lipase in complex with a phosphonate inhibitor
Analyse Crystal structure of dog gastric lipase in complex with a phosphonate inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K8Q
- Type
- protein
- Length
- 754 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triacylglycerol lipase, gastric
- EC
- 3.1.1.3
- UniProt
- P80035
- Ligands
- C11, NAG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triacylglycerol lipase, gastric (EC 3.1.1.3) | protein | 377 | 41% helix, 16% strand | P80035 |
Ligands and binding sites
- C11 · Undecyl-phosphinic acid butyl ester · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.79 | 0.85 | 44 | BOG, C11 |
| 2 | 528 | 0.77 | 0.84 | 46 | BOG, C11 |
| 3 | 282 | 0.72 | 0.86 | 40 | empty |
| 4 | 142 | 0.43 | 0.75 | 25 | empty |
| 5 | 138 | 0.42 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 425 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 covalent, 2 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- 1K8Q · Crystal structure of dog gastric lipase in complex with a phosphonate inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P80035 · AlphaFold monomer V2.0 prediction for gastric triacylglycerol lipase (P80035) · a predicted model of the same protein · 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 P80035
- Elsewhere: RCSB PDB 1K8Q · PDBe 1K8Q · UniProt P80035
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