Research workbench
Structural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich lipid-binding loop in lipoprotein lipase
Analyse Structural basis for the binding of monoclonal antibody 5D2 to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WN4
- Type
- protein
- Length
- 877 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5D2 Fab heavy chain; 5D2 Fab light chain; Lipoprotein lipase peptide
- UniProt
- P06858
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5D2 Fab heavy chain | protein | 214 | 7% helix, 52% strand | — |
| B | 5D2 Fab light chain | protein | 208 | 6% helix, 52% strand | — |
| C, D | Lipoprotein lipase peptide | protein | 11 | 45% helix, 0% strand | P06858 |
| H | 5D2 Fab heavy chain | protein | 221 | 7% helix, 51% strand | — |
| L | 5D2 Fab light chain | protein | 212 | 6% helix, 51% strand | — |
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 | 921 | 0.78 | 0.81 | 97 | empty |
| 2 | 668 | 0.64 | 0.74 | 80 | empty |
| 3 | 154 | 0.53 | 0.80 | 19 | empty |
| 4 | 58 | 0.38 | 0.80 | 17 | empty |
| 5 | 81 | 0.33 | 0.74 | 19 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1886 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1806 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 16 hydrogen bonds · protein-protein
- D–H · 488 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 401 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6WN4 · Structural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich… · the same entry in another collection · chain C against C, TM-score 1.00
- P06858 · AlphaFold monomer V2.0 prediction for lipoprotein lipase (P06858) · a predicted model of the same protein · chain C against A, TM-score 0.55
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
- Elsewhere: RCSB PDB 6WN4 · PDBe 6WN4 · UniProt P06858
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