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Hydroxynitrile lyase from passiflora edulis (pehnl)

Analyse Hydroxynitrile lyase from passiflora edulis (pehnl) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XZQ
Type: protein
Length: 1,278 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydroxynitrile lyase
UniProt: A0A1L7NZN4
Pockets: 16 · best druggability 0.74

Structure

x-ray diffraction · 7 distinct chains · 35% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hydroxynitrile lyase	protein	108	31% helix, 22% strand	A0A1L7NZN4
B, H, I, L	Hydroxynitrile lyase	protein	107	35% helix, 31% strand	A0A1L7NZN4
C, D, J	Hydroxynitrile lyase	protein	108	32% helix, 30% strand	A0A1L7NZN4
E	Hydroxynitrile lyase	protein	106	36% helix, 30% strand	A0A1L7NZN4
F	Hydroxynitrile lyase	protein	103	32% helix, 30% strand	A0A1L7NZN4
G	Hydroxynitrile lyase	protein	105	40% helix, 30% strand	A0A1L7NZN4
K	Hydroxynitrile lyase	protein	104	37% helix, 32% strand	A0A1L7NZN4

Pockets

16 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	772	0.74	0.79	61	empty
2	81	0.72	0.95	18	empty
3	71	0.71	0.95	18	empty
4	72	0.71	0.95	17	empty
5	74	0.71	0.95	17	empty

Interfaces

19 interfaces between chains.

C–D · 2154 Å² buried · 24 hydrogen bonds · protein-protein
I–J · 2097 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2031 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 1991 Å² buried · 26 hydrogen bonds · protein-protein
K–L · 1956 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

5XZQ · Hydroxynitrile lyase from Passiflora edulis (PeHNL) · 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 A0A1L7NZN4
Elsewhere: RCSB PDB 5XZQ · PDBe 5XZQ · UniProt A0A1L7NZN4

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