MolNFT v1 · #158993 · protein
Apo structure of wt lipoprotein lipase in complex with GPIHBP1 mutant N78D N82D produced in HEK293-F cells
6OAZ: “Apo structure of wt lipoprotein lipase in complex with GPIHBP1 mutant N78D N82D produced in HEK293-F cells”. X-ray diffraction, 2 ligands (NAG, CA), 19 pockets (best druggability 0.62). MolNFT v1 #158993 on GenesisL1: 3D structure…
- PDB
- 6OAZ
- Type
- protein
- Length
- 1,987 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
- NAG, CA
- Pockets
- 19 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lipoprotein lipase (EC 3.1.1.34) | protein | 416 | 22% helix, 34% strand | P06858 |
| E | Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 | protein | 83 | 0% helix, 53% strand | Q8IV16 |
| F | Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 | protein | 79 | 4% helix, 51% strand | Q8IV16 |
| G | Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 | protein | 81 | 4% helix, 54% strand | Q8IV16 |
| H | Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 | protein | 80 | 0% helix, 55% strand | Q8IV16 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, E, B, F, C, G, D, H
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.62 | 0.77 | 63 | empty |
| 2 | 52 | 0.47 | 0.85 | 17 | empty |
| 3 | 137 | 0.43 | 0.76 | 22 | empty |
| 4 | 170 | 0.43 | 0.74 | 26 | empty |
| 5 | 60 | 0.43 | 0.82 | 18 | empty |
Interfaces
12 interfaces between chains.
- C–G · 1023 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1022 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1016 Ų buried · 13 hydrogen bonds · protein-protein
- D–H · 984 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 795 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6OAZ · Apo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced… · the same entry in another collection · chain H against H, 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 1.00
- Q8IV16 · AlphaFold monomer V2.0 prediction for glycosylphosphatidylinositol- anchored high density… · a predicted model of the same protein · chain G 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 6OAZ · PDBe 6OAZ · UniProt P06858 · UniProt Q8IV16
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