MolNFT v1 · #52499 · protein

Wt PCSK9-deltac bound to wt EGF-a of ldlr

2W2M · Proprotein convertase SUBTILISIN/KEXIN type 9: “Wt PCSK9-deltac bound to wt EGF-a of ldlr”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.37). MolNFT v1 #52499 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2W2M
Type: protein
Length: 418 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: 2 · best druggability 0.37

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-)	protein	277	30% helix, 24% strand	Q8NBP7
E	Low-density lipoprotein receptor	protein	49	14% helix, 29% strand	P01130
P	Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-)	protein	92	30% helix, 39% strand	Q8NBP7

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, E

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.37	0.75	21	empty
2	81	0.30	0.73	19	empty

Interfaces

2 interfaces between chains.

A–P · 1330 Å² buried · 30 hydrogen bonds · protein-protein
A–E · 512 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

2W2M · Wt PCSK9-deltac bound to wt EGF-a of ldlr · 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 0.83

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 2W2M · PDBe 2W2M · UniProt Q8NBP7 · UniProt P01130

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