Research workbench
Anti-PCSK9 Fab 6E2 bound to the N-terminal peptide from PCSK9, unmodified
Analyse Anti-PCSK9 Fab 6E2 bound to the N-terminal peptide from PCSK9, unmodified in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E4Y
- Type
- protein
- Length
- 442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6E2 heavy chain; 6E2 light chain; Proprotein convertase SUBTILISIN/KEXIN type 9
- UniProt
- A0A097PUG4, Q8NBP7
- Ligands
- ZN, CL
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 6E2 heavy chain | protein | 210 | 10% helix, 53% strand | — |
| L | 6E2 light chain | protein | 218 | 5% helix, 50% strand | A0A097PUG4 |
| P | Proprotein convertase SUBTILISIN/KEXIN type 9 | protein | 14 | 64% helix, 0% strand | Q8NBP7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.63 | 0.88 | 21 | empty |
| 2 | 54 | 0.51 | 0.88 | 24 | empty |
| 3 | 199 | 0.49 | 0.76 | 36 | empty |
| 4 | 170 | 0.45 | 0.75 | 29 | empty |
| 5 | 77 | 0.35 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1735 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 457 Ų buried · 8 hydrogen bonds · protein-protein
- L–P · 189 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 6E4Y · Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9, unmodified · the same entry in another collection · chain H against H, 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 A0A097PUG4
- Every structure of UniProt Q8NBP7
- Elsewhere: RCSB PDB 6E4Y · PDBe 6E4Y · UniProt A0A097PUG4 · UniProt Q8NBP7
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