Research workbench
PCSK9 in complex with PCSK9I a 13MER cyclic peptide ldlr disruptor
Analyse PCSK9 in complex with PCSK9I a 13MER cyclic peptide ldlr disruptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KFA
- Type
- protein
- Length
- 572 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9 propeptide; Proprotein convertase…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- WCM, ACE, NEH, CA
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 propeptide | protein | 92 | 30% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 471 | 18% helix, 38% strand | Q8NBP7 |
| D | 1-[2,6,10.14-tetramethyl-hexadecan-16-yl]-2-[2,10,14- trimethylhexadecan-16-YL]GLYCEROL | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- WCM · (2S)-2-amino-3-(biphenyl-4-yl)-N-methyl-N-[(2S)-1-oxopropan-2-yl]propanamide (non-preferred name) · ligand · 2 copies · chains A, B, D
- ACE · Acetyl group · ligand · chains B, D
- NEH · Ethanamine · ligand · chains B, D
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.73 | 0.82 | 59 | CA |
| 2 | 215 | 0.67 | 0.85 | 43 | empty |
| 3 | 131 | 0.53 | 0.81 | 26 | WCM |
| 4 | 52 | 0.30 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1355 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 418 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 5 covalent (disulfide, covalent ligand).
Compared structures
- 7KFA · PCSK9 in complex with PCSK9i a 13mer cyclic peptide LDLR disruptor · 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 7KFA · PDBe 7KFA · UniProt Q8NBP7
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