Research workbench
PCSK9 complex with FAB33
Analyse PCSK9 complex with FAB33 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VL7
- Type
- protein
- Length
- 958 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; FAB33 heavy chain; FAB33 light chain
- EC
- 3.4.21.-
- UniProt
- Q8NBP7, Q7Z3Y4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 92 | 30% helix, 41% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 437 | 18% helix, 39% strand | Q8NBP7 |
| H | FAB33 heavy chain | protein | 219 | 0% helix, 47% strand | — |
| L | FAB33 light chain | protein | 210 | 5% helix, 46% strand | Q7Z3Y4 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.75 | 0.81 | 88 | empty |
| 2 | 319 | 0.61 | 0.78 | 41 | empty |
| 3 | 256 | 0.48 | 0.74 | 38 | empty |
| 4 | 155 | 0.40 | 0.73 | 27 | empty |
| 5 | 109 | 0.37 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1893 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1347 Ų buried · 30 hydrogen bonds · protein-protein
- B–H · 762 Ų buried · 11 hydrogen bonds · protein-protein
- B–L · 328 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5VL7 · PCSK9 complex with Fab33 · 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 Q7Z3Y4
- Elsewhere: RCSB PDB 5VL7 · PDBe 5VL7 · UniProt Q8NBP7 · UniProt Q7Z3Y4
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