Research workbench
PCSK9 in complex with compound 4
Analyse PCSK9 in complex with compound 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U2N
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Homo sapiens
- Molecule
- Proprotein convertase subtilisin/kexin type 9
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- PV7
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.15 · 2 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase subtilisin/kexin type 9 (EC 3.4.21.-) | protein | 92 | 32% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase subtilisin/kexin type 9 (EC 3.4.21.-) | protein | 479 | 17% helix, 38% strand | Q8NBP7 |
Ligands and binding sites
- PV7 · 4-{[(1R)-6-methoxy-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.74 | 0.82 | 64 | PV7 |
| 2 | 305 | 0.68 | 0.83 | 51 | empty |
| 3 | 211 | 0.51 | 0.76 | 38 | empty |
| 4 | 57 | 0.35 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1398 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
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 Q8NBP7
- Elsewhere: RCSB PDB 6U2N · PDBe 6U2N · UniProt Q8NBP7
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