Research workbench

Prolyl oligopeptidase B from galerina marginata - apo protein

Analyse Prolyl oligopeptidase B from galerina marginata - apo protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N4F
Type: protein
Length: 703 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prolyl oligopeptidase
UniProt: H2E7Q8
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prolyl oligopeptidase	protein	703	22% helix, 33% strand	H2E7Q8

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A

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	682	0.70	0.77	64	empty
2	313	0.54	0.75	38	empty
3	134	0.42	0.75	21	GOL
4	71	0.39	0.79	16	empty
5	60	0.29	0.74	15	empty

Compared structures

5N4F · Prolyl oligopeptidase B from Galerina marginata - apo protein · the same entry in another collection · chain A against A, TM-score 1.00
H2E7Q8 · AlphaFold monomer V2.0 prediction for dual function macrocyclase- peptidase popb (H2E7Q8) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 H2E7Q8
Elsewhere: RCSB PDB 5N4F · PDBe 5N4F · UniProt H2E7Q8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.