Research workbench

PCSK9:EGFA (pH 7.4)

Analyse PCSK9:EGFA (pH 7.4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GCX
Type: protein
Length: 567 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proprotein convertase SUBTILISIN/KEXIN type 9; Low-density lipoprotein receptor
EC: 3.4.21.-
UniProt: Q8NBP7, P01130
Ligands: CA
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-)	protein	92	30% helix, 39% strand	Q8NBP7
A	Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-)	protein	434	20% helix, 36% strand	Q8NBP7
E	Low-density lipoprotein receptor	protein	41	17% helix, 24% strand	P01130

Ligands and binding sites

CA · Calcium ion · metal · chains E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	711	0.76	0.81	102	empty
2	54	0.41	0.82	17	empty
3	86	0.38	0.76	20	empty
4	51	0.29	0.75	13	empty

Interfaces

2 interfaces between chains.

P–A · 1371 Å² buried · 29 hydrogen bonds · protein-protein
A–E · 508 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3GCX · PCSK9:EGFA (pH 7.4) · the same entry in another collection · chain P against P, TM-score 1.00
P01130 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor (P01130) · a predicted model of the same protein · chain E against A, TM-score 0.90

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
Every structure of UniProt P01130
Elsewhere: RCSB PDB 3GCX · PDBe 3GCX · UniProt Q8NBP7 · UniProt P01130

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