Research workbench
PCSK9 J16 Fab complex
Analyse PCSK9 J16 Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SQO
- Type
- protein
- Length
- 1,007 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; J16 heavy chain; J16 light chain; PCSK9…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 491 | 18% helix, 37% strand | Q8NBP7 |
| H | J16 heavy chain | protein | 211 | 4% helix, 51% strand | — |
| L | J16 light chain | protein | 213 | 7% helix, 51% strand | — |
| P | PCSK9 prodomain (EC 3.4.21.-) | protein | 92 | 28% helix, 39% strand | Q8NBP7 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.72 | 0.81 | 76 | empty |
| 2 | 382 | 0.72 | 0.83 | 55 | empty |
| 3 | 568 | 0.61 | 0.73 | 59 | empty |
| 4 | 347 | 0.57 | 0.75 | 43 | empty |
| 5 | 107 | 0.40 | 0.76 | 24 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1849 Ų buried · 21 hydrogen bonds · protein-protein
- A–P · 1367 Ų buried · 31 hydrogen bonds · protein-protein
- A–H · 469 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 423 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3SQO · PCSK9 J16 Fab complex · the same entry in another collection · chain A against A, TM-score 1.00
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 3SQO · PDBe 3SQO · UniProt Q8NBP7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.