MolNFT v1 · #47633 · protein
Crystal structure of PCSK9
2P4E · Proprotein convertase SUBTILISIN/KEXIN type 9: “Crystal structure of PCSK9”. X-ray diffraction, 1 ligand (HG), 4 pockets (best druggability 0.74). MolNFT v1 #47633 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2P4E
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- HG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 92 | 30% helix, 39% strand | Q8NBP7 |
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 494 | 18% helix, 38% strand | Q8NBP7 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 2 copies · chains P, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.74 | 0.81 | 65 | empty |
| 2 | 367 | 0.71 | 0.83 | 51 | empty |
| 3 | 190 | 0.47 | 0.75 | 30 | empty |
| 4 | 67 | 0.32 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- P–A · 1339 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2P4E · Crystal Structure of PCSK9 · the same entry in another collection · chain P against P, 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 2P4E · PDBe 2P4E · UniProt Q8NBP7
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