Research workbench
PCSK9:FAB complex with dextran sulfate
Analyse PCSK9:FAB complex with dextran sulfate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OCA
- Type
- protein
- Length
- 1,020 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: heavy…
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- TWD, TWA, NA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 15% 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 | 495 | 17% helix, 37% strand | Q8NBP7 |
| H | Fab from ldlr competitive antibody: heavy chain | protein | 219 | 10% helix, 53% strand | — |
| L | Fab from ldlr competitive antibody: light chain | protein | 214 | 8% helix, 51% strand | — |
Ligands and binding sites
- TWD · 2,3-di-O-sulfo-alpha-L-glucopyranose · ligand · chains A
- TWA · 2,3,4-tri-O-sulfo-beta-D-altropyranose · ligand · chains A
- NA · Sodium ion · metal · 2 copies · 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 | 89 | 0.77 | 0.99 | 25 | empty |
| 2 | 747 | 0.76 | 0.81 | 88 | empty |
| 3 | 310 | 0.70 | 0.84 | 51 | empty |
| 4 | 407 | 0.58 | 0.75 | 63 | empty |
| 5 | 147 | 0.46 | 0.77 | 24 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1607 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1322 Ų buried · 28 hydrogen bonds · protein-protein
- B–H · 1036 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 180 Ų buried · 1 hydrogen bond · protein-protein
- B–L · 139 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5OCA · PCSK9:Fab Complex with Dextran Sulfate · 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 5OCA · PDBe 5OCA · UniProt Q8NBP7
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