Research workbench

Structural and mechanistic analysis of two prolyl endopeptidases: role of inter-domain dynamics in catalysis and specificity

Analyse Structural and mechanistic analysis of two prolyl endopeptidases: role of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YR2
Type: protein
Length: 680 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prolyl oligopeptidase
EC: 3.4.21.26
UniProt: Q9ZNM8
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prolyl oligopeptidase (EC 3.4.21.26)	protein	680	22% helix, 35% strand	Q9ZNM8

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

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	403	0.59	0.76	34	empty
2	151	0.48	0.77	30	empty
3	199	0.47	0.75	23	empty
4	57	0.27	0.74	15	empty

Compared structures

1YR2 · Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Inter-Domain… · the same entry in another collection · chain A against A, 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 Q9ZNM8
Elsewhere: RCSB PDB 1YR2 · PDBe 1YR2 · UniProt Q9ZNM8

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