Research workbench
PCSK9 in complex with a Fab and compound 8
Analyse PCSK9 in complex with a Fab and compound 8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U38
- Type
- protein
- Length
- 1,000 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; Fab heavy chain; Fab light chain
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- PVJ
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 92 | 28% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 482 | 17% helix, 38% strand | Q8NBP7 |
| H | Fab heavy chain | protein | 216 | 8% helix, 54% strand | — |
| L | Fab light chain | protein | 210 | 6% helix, 49% strand | — |
Ligands and binding sites
- PVJ · 2-fluoro-4-{[(1R)-1-methyl-6-{[(2S)-oxan-2-yl]methoxy}-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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.75 | 0.81 | 70 | PVJ |
| 2 | 273 | 0.69 | 0.84 | 42 | empty |
| 3 | 275 | 0.50 | 0.74 | 45 | empty |
| 4 | 136 | 0.46 | 0.77 | 20 | empty |
| 5 | 142 | 0.45 | 0.76 | 30 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1662 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 24 hydrogen bonds · protein-protein
- B–L · 532 Ų buried · 8 hydrogen bonds · protein-protein
- B–H · 134 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6U38 · PCSK9 in complex with a Fab and compound 8 · 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 6U38 · PDBe 6U38 · UniProt Q8NBP7
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