MolNFT v1 · #165682 · protein
PCSK9 in complex with a Fab and compound 14
6U36 · Proprotein convertase SUBTILISIN/KEXIN type 9: “PCSK9 in complex with a Fab and compound 14”. X-ray diffraction, 1 ligand (PVM), 9 pockets (best druggability 0.75). MolNFT v1 #165682 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6U36
- Type
- protein
- Length
- 996 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
- PVM
- 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 | 29% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 481 | 17% helix, 39% strand | Q8NBP7 |
| H | Fab heavy chain | protein | 213 | 8% helix, 54% strand | — |
| L | Fab light chain | protein | 210 | 7% helix, 50% strand | — |
Ligands and binding sites
- PVM · 2-fluoro-4-{[(1R)-6-(2-{4-[1-(4-methoxyphenyl)-5-methyl-6-oxo-1,6-dihydropyridazin-3-yl]-1H-1,2,3-triazol-1-yl}ethoxy)-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
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 | 612 | 0.75 | 0.82 | 73 | PVM |
| 2 | 225 | 0.68 | 0.85 | 39 | empty |
| 3 | 125 | 0.61 | 0.86 | 26 | empty |
| 4 | 232 | 0.49 | 0.74 | 32 | empty |
| 5 | 114 | 0.43 | 0.77 | 19 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1627 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1340 Ų buried · 27 hydrogen bonds · protein-protein
- B–L · 534 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 128 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6U36 · PCSK9 in complex with a Fab and compound 14 · 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 6U36 · PDBe 6U36 · UniProt Q8NBP7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.