MolNFT v1 · #137346 · protein
PCSK9 complex with ldlr antagonist peptide and FAB7G7
5VLP · Proprotein convertase SUBTILISIN/KEXIN type 9: “PCSK9 complex with ldlr antagonist peptide and FAB7G7”. X-ray diffraction, 2 ligands (ACE, NA), 8 pockets (best druggability 0.73). MolNFT v1 #137346 on GenesisL1: 3D structure…
- PDB
- 5VLP
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; FAB7G7 heavy chain; FAB7G7 light chain…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7, A0A0U5BC76
- Ligands
- ACE, NA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 577 | 19% helix, 38% strand | Q8NBP7 |
| H | FAB7G7 heavy chain | protein | 220 | 7% helix, 55% strand | — |
| L | FAB7G7 light chain | protein | 214 | 6% helix, 50% strand | A0A0U5BC76 |
| Z | Ldlr antagonist peptide | protein | 16 | 31% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.73 | 0.83 | 64 | NA |
| 2 | 297 | 0.71 | 0.85 | 38 | empty |
| 3 | 480 | 0.60 | 0.75 | 63 | empty |
| 4 | 266 | 0.58 | 0.78 | 29 | empty |
| 5 | 275 | 0.51 | 0.74 | 30 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1966 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 827 Ų buried · 14 hydrogen bonds · protein-protein
- A–Z · 698 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 348 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 5VLP · PCSK9 complex with LDLR antagonist peptide and Fab7G7 · 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
- Every structure of UniProt A0A0U5BC76
- Elsewhere: RCSB PDB 5VLP · PDBe 5VLP · UniProt Q8NBP7 · UniProt A0A0U5BC76
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