MolNFT v1 · #140094 · protein

C-terminal peptide depleted mutant of hydroxynitrile lyase from passiflora edulis (pehnl)

5XZT: “C-terminal peptide depleted mutant of hydroxynitrile lyase from passiflora edulis (pehnl)”. X-ray diffraction, 19 pockets (best druggability 0.75). MolNFT v1 #140094 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XZT
Type: protein
Length: 1,255 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydroxynitrile lyase
UniProt: A0A1L7NZN4
Pockets: 19 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F, G, I, K, L	Hydroxynitrile lyase	protein	104	36% helix, 34% strand	A0A1L7NZN4
C, H	Hydroxynitrile lyase	protein	107	36% helix, 32% strand	A0A1L7NZN4
D, E	Hydroxynitrile lyase	protein	105	36% helix, 33% strand	A0A1L7NZN4
J	Hydroxynitrile lyase	protein	103	39% helix, 35% strand	A0A1L7NZN4

Ligands and binding sites

HEZ · Hexane-1,6-diol · additive · 19 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.75	0.97	16	HEZ
2	65	0.74	0.98	15	HEZ
3	82	0.73	0.95	20	HEZ
4	71	0.71	0.95	17	HEZ
5	518	0.68	0.79	40	empty

Interfaces

18 interfaces between chains.

G–H · 1797 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1790 Å² buried · 29 hydrogen bonds · protein-protein
K–L · 1787 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 1761 Å² buried · 31 hydrogen bonds · protein-protein
I–J · 1758 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

5XZT · C-terminal peptide depleted mutant of 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 5XZT · PDBe 5XZT · UniProt A0A1L7NZN4

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