Research workbench
Compound 2 bound structure of wt lipoprotein lipase in complex with GPIHBP1 mutant N78D N82D produced in HEK293-F cells
Analyse Compound 2 bound structure of wt lipoprotein lipase in complex with GPIHBP1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OB0
- Type
- protein
- Length
- 2,094 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein lipase; Glycosylphosphatidylinositol-anchored high density…
- EC
- 3.1.1.34
- UniProt
- P06858, Q8IV16
- Ligands
- M3D, NAG, CA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lipoprotein lipase (EC 3.1.1.34) | protein | 442 | 24% helix, 31% strand | P06858 |
| E | Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 | protein | 83 | 4% helix, 57% strand | Q8IV16 |
| F, G, H | Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 | protein | 81 | 0% helix, 56% strand | Q8IV16 |
Ligands and binding sites
- M3D · 7-(3-cyano-4-hydroxyphenyl)-N-[2-(morpholin-4-yl) ethyl]dibenzo[b,f]oxepine-10-carboxamide · ligand · 8 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.77 | 0.80 | 68 | M3D |
| 2 | 859 | 0.77 | 0.80 | 75 | M3D |
| 3 | 866 | 0.76 | 0.80 | 86 | M3D |
| 4 | 824 | 0.76 | 0.80 | 71 | M3D |
| 5 | 386 | 0.63 | 0.78 | 47 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1355 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1268 Ų buried · 17 hydrogen bonds · protein-protein
- D–H · 1006 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1004 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 1001 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6OB0 · Compound 2 bound structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8IV16 · AlphaFold monomer V2.0 prediction for glycosylphosphatidylinositol- anchored high density… · a predicted model of the same protein · chain F against A, TM-score 0.99
- P06858 · AlphaFold monomer V2.0 prediction for lipoprotein lipase (P06858) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P06858
- Every structure of UniProt Q8IV16
- Elsewhere: RCSB PDB 6OB0 · PDBe 6OB0 · UniProt P06858 · UniProt Q8IV16
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.