Research workbench
Crystal structure of PCSK9 in complex with Fab from ldlr competitive antibody
Analyse Crystal structure of PCSK9 in complex with Fab from ldlr competitive antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H42
- Type
- protein
- Length
- 1,019 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9; Fab from ldlr competitive antibody: light…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- NA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 44% 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 | 17% helix, 39% strand | Q8NBP7 |
| L | Fab from ldlr competitive antibody: light chain | protein | 214 | 8% helix, 50% strand | — |
| H | Fab from ldlr competitive antibody: heavy chain | protein | 221 | 8% helix, 52% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.77 | 0.99 | 25 | empty |
| 2 | 716 | 0.75 | 0.81 | 86 | NA |
| 3 | 318 | 0.71 | 0.84 | 46 | empty |
| 4 | 333 | 0.56 | 0.75 | 46 | empty |
| 5 | 138 | 0.45 | 0.76 | 25 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1625 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1342 Ų buried · 28 hydrogen bonds · protein-protein
- B–H · 1037 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 180 Ų buried · 1 hydrogen bond · protein-protein
- B–L · 142 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3H42 · Crystal structure of PCSK9 in complex with Fab from LDLR competitive antibody · 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 3H42 · PDBe 3H42 · UniProt Q8NBP7
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