Research workbench
PCSK9-deltac D374Y mutant bound to wt EGF-a of ldlr
Analyse PCSK9-deltac D374Y mutant bound to wt EGF-a of ldlr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W2O
- Type
- protein
- Length
- 413 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
- EC
- 3.4.21.-
- UniProt
- Q8NBP7, P01130
- Ligands
- CA
- Pockets
- 4 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 274 | 31% helix, 23% strand | Q8NBP7 |
| E | Low-density lipoprotein receptor | protein | 47 | 9% helix, 30% strand | P01130 |
| P | Proprotein convertase SUBTILISIN/KEXIN type 9 | protein | 92 | 29% helix, 39% strand | Q8NBP7 |
Ligands and binding sites
- CA · Calcium ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.34 | 0.74 | 15 | empty |
| 2 | 63 | 0.31 | 0.75 | 14 | empty |
| 3 | 58 | 0.28 | 0.74 | 17 | empty |
| 4 | 61 | 0.28 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–P · 1300 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 562 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 P01130
- Elsewhere: RCSB PDB 2W2O · PDBe 2W2O · UniProt Q8NBP7 · UniProt P01130
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