Research workbench
Complete PCSK9 C-ter domain in complex with vhh P1.40
Analyse Complete PCSK9 C-ter domain in complex with vhh P1.40 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ANQ
- Type
- protein
- Length
- 349 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; Vhh P1.40 minibody anti-cter PCSK9
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- NAG, FUC, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 222 | 0% helix, 55% strand | Q8NBP7 |
| B | Vhh P1.40 minibody anti-cter PCSK9 | protein | 127 | 7% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.72 | 0.84 | 55 | empty |
| 2 | 121 | 0.58 | 0.85 | 29 | SO4 |
| 3 | 78 | 0.40 | 0.79 | 20 | empty |
| 4 | 69 | 0.36 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 913 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7ANQ · Complete PCSK9 C-ter domain in complex with VHH P1.40 · 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 7ANQ · PDBe 7ANQ · UniProt Q8NBP7
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