MolNFT v1 · #179748 · protein
PCSK9 in complex with a cyclic peptide ldlr disruptor
7KEV · Proprotein convertase SUBTILISIN/KEXIN type 9 propeptide: “PCSK9 in complex with a cyclic peptide ldlr disruptor”. X-ray diffraction, 4 ligands (WCM, ACE, CA), 3 pockets (best druggability 0.73). MolNFT v1 #179748 on GenesisL1: 3D…
- PDB
- 7KEV
- Type
- protein
- Length
- 573 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, CA, NH2
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 37% 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 | 17% helix, 38% strand | Q8NBP7 |
| C | Cyclic peptide ldlr disruptor | protein | 10 | 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, C
- ACE · Acetyl group · ligand · chains B, C
- CA · Calcium ion · metal · chains B
- NH2 · Amino group · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.73 | 0.82 | 56 | CA |
| 2 | 197 | 0.68 | 0.86 | 44 | empty |
| 3 | 142 | 0.54 | 0.81 | 26 | WCM |
Interfaces
3 interfaces between chains.
- A–B · 1341 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 471 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 7KEV · PCSK9 in complex with a 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 7KEV · PDBe 7KEV · UniProt Q8NBP7
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