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Prolyl oligopeptidase B from galerina marginata bound to 35MER hydrolysis and macrocyclization substrate - S577A mutant

Analyse Prolyl oligopeptidase B from galerina marginata bound to 35MER hydrolysis and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N4C
Type: protein
Length: 3,014 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prolyl oligopeptidase; Alpha-amanitin proprotein
UniProt: H2E7Q8, H2E7Q5
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 7 distinct chains · 22% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prolyl oligopeptidase	protein	722	22% helix, 32% strand	H2E7Q8
E	Alpha-amanitin proprotein	protein	32	25% helix, 0% strand	H2E7Q5
B	Prolyl oligopeptidase	protein	721	22% helix, 32% strand	H2E7Q8
C	Prolyl oligopeptidase	protein	721	22% helix, 32% strand	H2E7Q8
D	Prolyl oligopeptidase	protein	720	22% helix, 32% strand	H2E7Q8
F	Alpha-amanitin proprotein	protein	32	25% helix, 0% strand	H2E7Q5
G, H	Alpha-amanitin proprotein	protein	33	24% helix, 0% strand	H2E7Q5

Ligands and binding sites

GOL · Glycerol · additive · chains D

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	954	0.89	0.91	129	empty
2	748	0.88	0.91	95	empty
3	700	0.87	0.91	95	empty
4	953	0.87	0.89	104	empty
5	523	0.87	0.93	102	empty

Interfaces

9 interfaces between chains.

B–F · 2026 Å² buried · 20 hydrogen bonds · protein-protein
D–H · 2021 Å² buried · 21 hydrogen bonds · protein-protein
C–G · 1996 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 1904 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 978 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5N4C · Prolyl oligopeptidase B from Galerina marginata bound to 35mer hydrolysis and… · the same entry in another collection · chain H against H, 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 B 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 H2E7Q8
Every structure of UniProt H2E7Q5
Elsewhere: RCSB PDB 5N4C · PDBe 5N4C · UniProt H2E7Q8 · UniProt H2E7Q5

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