Research workbench
PCSK9 in complex with an inhibitor
Analyse PCSK9 in complex with an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8FVM
- Type
- protein
- Length
- 578 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.852
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Proprotein convertase subtilisin/kexin type 9; DGN-DVA-YC3-GLU-PRO-THR-THR-PHE-MAA-A1BC0…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- CA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.852 · 3 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 | 30% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase subtilisin/kexin type 9 (EC 3.4.21.-) | protein | 476 | 17% helix, 39% strand | Q8NBP7 |
| C | DGN-DVA-YC3-GLU-PRO-THR-THR-PHE-MAA-A1BC0 inhibitor | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.72 | 0.83 | 51 | CA |
| 2 | 284 | 0.70 | 0.85 | 43 | empty |
| 3 | 164 | 0.48 | 0.76 | 26 | empty |
| 4 | 56 | 0.36 | 0.80 | 18 | empty |
| 5 | 70 | 0.30 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1377 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 629 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 163 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 modified, 2 d-amino (disulfide, nonstandard, D-amino acid).
Compared structures
- Q8NBP7 · AlphaFold monomer V2.0 prediction for proprotein convertase SUBTILISIN/KEXIN type 9… · a predicted model of the same protein · chain A 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 Q8NBP7
- Elsewhere: RCSB PDB 8FVM · PDBe 8FVM · UniProt Q8NBP7
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