Research workbench
An antibody against the C-terminal domain of PCSK9 lowers LDL cholesterol levels in vivo
Analyse An antibody against the C-terminal domain of PCSK9 lowers LDL cholesterol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K8R
- Type
- protein
- Length
- 1,461 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; FAB1, light chain; FAB1, heavy chain…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 92 | 30% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 492 | 18% helix, 38% strand | Q8NBP7 |
| C | FAB1, light chain | protein | 213 | 5% helix, 45% strand | — |
| D | FAB1, heavy chain | protein | 229 | 3% helix, 48% strand | — |
| H | FAB3H42, heavy chain | protein | 221 | 4% helix, 52% strand | — |
| L | FAB3H42, light chain | protein | 214 | 7% helix, 50% strand | — |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.76 | 0.98 | 24 | empty |
| 2 | 783 | 0.75 | 0.80 | 94 | empty |
| 3 | 453 | 0.73 | 0.83 | 70 | empty |
| 4 | 512 | 0.60 | 0.74 | 45 | empty |
| 5 | 258 | 0.54 | 0.76 | 37 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1918 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1658 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1322 Ų buried · 32 hydrogen bonds · protein-protein
- B–H · 1051 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 613 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 4K8R · An Antibody Against the C-terminal Domain of PCSK9 lowers LDL Cholesterol Levels in vivo · 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 4K8R · PDBe 4K8R · UniProt Q8NBP7
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