MolNFT v1 · #74729 · protein
The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation
3P5C · Proprotein convertase SUBTILISIN/KEXIN type 9: “The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation”. X-ray diffraction, 1 ligand (CA), 11 pockets (best druggability 0.79). MolNFT v1 #74729 on…
- PDB
- 3P5C
- Type
- protein
- Length
- 1,028 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; Low density lipoprotein receptor variant
- EC
- 3.4.21.-
- UniProt
- Q8NBP7, Q59FQ1
- Ligands
- CA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 92 | 23% helix, 39% strand | Q8NBP7 |
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 496 | 15% helix, 37% strand | Q8NBP7 |
| L | Low density lipoprotein receptor variant | protein | 440 | 2% helix, 38% strand | Q59FQ1 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.79 | 0.94 | 34 | empty |
| 2 | 283 | 0.75 | 0.88 | 43 | empty |
| 3 | 563 | 0.72 | 0.80 | 64 | CA |
| 4 | 366 | 0.67 | 0.80 | 44 | empty |
| 5 | 157 | 0.53 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- P–A · 1429 Ų buried · 30 hydrogen bonds · protein-protein
- A–L · 548 Ų buried · 9 hydrogen bonds · protein-protein
- P–L · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3P5C · The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation · 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
- Every structure of UniProt Q59FQ1
- Elsewhere: RCSB PDB 3P5C · PDBe 3P5C · UniProt Q8NBP7 · UniProt Q59FQ1
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