MolNFT v1 · #158988 · protein
Apo structure of wt lipoprotein lipase in complex with GPIHBP1 mutant N78D N82D produced in gnti-deficient HEK293-F cells
6OAU: “Apo structure of wt lipoprotein lipase in complex with GPIHBP1 mutant N78D N82D produced in gnti-deficient…”. X-ray diffraction, 2 ligands (NAG, CA), 7 pockets (best druggability 0.62). MolNFT v1 #158988 on GenesisL1: 3D structure…
- PDB
- 6OAU
- Type
- protein
- Length
- 1,007 residues
- Chains
- 4
- 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
- NAG, CA
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipoprotein lipase (EC 3.1.1.34) | protein | 422 | 22% helix, 33% strand | P06858 |
| C | Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 | protein | 81 | 0% helix, 56% strand | Q8IV16 |
| D | Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 | protein | 82 | 4% helix, 55% strand | Q8IV16 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.62 | 0.77 | 53 | empty |
| 2 | 180 | 0.56 | 0.80 | 29 | empty |
| 3 | 130 | 0.45 | 0.77 | 22 | empty |
| 4 | 110 | 0.42 | 0.77 | 22 | empty |
| 5 | 60 | 0.42 | 0.82 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1006 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 997 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 887 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6OAU · Apo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced… · the same entry in another collection · chain A against A, TM-score 1.00
- P06858 · AlphaFold monomer V2.0 prediction for lipoprotein lipase (P06858) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8IV16 · AlphaFold monomer V2.0 prediction for glycosylphosphatidylinositol- anchored high density… · a predicted model of the same protein · chain C 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 P06858
- Every structure of UniProt Q8IV16
- Elsewhere: RCSB PDB 6OAU · PDBe 6OAU · UniProt P06858 · UniProt Q8IV16
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