MolNFT v1 · #157317 · protein
Anti-PCSK9 Fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K)
6MV5 · Anti-PCSK9 Fab 6E2 heavy chain: “Anti-PCSK9 Fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K)”. X-ray diffraction, 4 ligands (ACE, ZN, SO4), 5 pockets (best druggability 0.66). MolNFT v1 #157317 on GenesisL1: 3D structure…
- PDB
- 6MV5
- Type
- protein
- Length
- 447 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-PCSK9 Fab 6E2 heavy chain; Anti-PCSK9 Fab 6E2 light chain; Proprotein convertase…
- UniProt
- A0A097PUG4, Q8NBP7
- Ligands
- ACE, ZN, SO4, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-PCSK9 Fab 6E2 heavy chain | protein | 210 | 10% helix, 52% strand | — |
| L | Anti-PCSK9 Fab 6E2 light chain | protein | 218 | 5% helix, 49% strand | A0A097PUG4 |
| P | Proprotein convertase SUBTILISIN/KEXIN type 9 | protein | 19 | 47% helix, 0% strand | Q8NBP7 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains H, P
- ZN · Zinc ion · metal · 4 copies · chains H, P, L
- SO4 · Sulfate ion · ion · 2 copies · chains H, P, L
- CL · Chloride ion · ion · chains H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.66 | 0.89 | 24 | empty |
| 2 | 283 | 0.52 | 0.74 | 47 | empty |
| 3 | 174 | 0.45 | 0.74 | 32 | empty |
| 4 | 121 | 0.40 | 0.75 | 21 | empty |
| 5 | 77 | 0.31 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1664 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 677 Ų buried · 15 hydrogen bonds · protein-protein
- L–P · 237 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, phosphorylation).
Compared structures
- 6MV5 · Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K) · 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 6MV5 · PDBe 6MV5 · UniProt A0A097PUG4 · UniProt Q8NBP7
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