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Anti-PCSK9 Fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K)

Analyse Anti-PCSK9 Fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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.

Pocket	Volume (Å³)	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 Å² buried · 15 hydrogen bonds · protein-protein
H–P · 677 Å² buried · 15 hydrogen bonds · protein-protein
L–P · 237 Å² 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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