MolNFT v1 · #187212 · protein
PCSK9 in complex with compound 19
7S5G · Propeptide of proprotein convertase SUBTILISIN/KEXIN type 9: “PCSK9 in complex with compound 19”. X-ray diffraction, 4 ligands (B74, MPT, DHL), 1 pocket (best druggability 0.45). MolNFT v1 #187212 on GenesisL1: 3D structure, binding…
- PDB
- 7S5G
- Type
- protein
- Length
- 387 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propeptide of proprotein convertase SUBTILISIN/KEXIN type 9; Proprotein convertase…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- B74, MPT, DHL, 89N
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Propeptide of proprotein convertase SUBTILISIN/KEXIN type 9 | protein | 92 | 30% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 287 | 31% helix, 24% strand | Q8NBP7 |
| C | 8VH-Z02-ala-dal-phe-ftr-pro-thr-0A1-3WX | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- B74 · (3-methylphenyl)methanol · ligand · chains B, C
- MPT · Beta-mercaptopropionic acid · ligand · chains B, C
- DHL · 2-amino-ethanethiol · ligand · chains B, C
- 89N · (2E)-but-2-ene-1,4-diol · ligand · chains B, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.45 | 0.79 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1321 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 3 disulfide, 3 modified, 1 d-amino (covalent ligand, disulfide, nonstandard, D-amino acid).
Compared structures
- 7S5G · PCSK9 in complex with compound 19 · 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 7S5G · PDBe 7S5G · UniProt Q8NBP7
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