MolNFT v1 · #117307 · protein

Hydroxynitrile lyase from the fern davallia tyermanii in complex with (R)-mandelonitrile / benzaldehyde

5E4B: “Hydroxynitrile lyase from the fern davallia tyermanii in complex with (R)-mandelonitrile / benzaldehyde”. X-ray diffraction, 2 ligands (HBX, MXN), 4 pockets (best druggability 0.70). MolNFT v1 #117307 on GenesisL1: 3D structure…

PDB: 5E4B
Type: protein
Length: 352 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydroxynitrile lyase
Ligands: HBX, MXN
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hydroxynitrile lyase	protein	176	28% helix, 39% strand	—

Ligands and binding sites

HBX · benzaldehyde · ligand · 2 copies · chains A, B
MXN · (2R)-hydroxy(phenyl)ethanenitrile · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	265	0.70	0.85	49	empty
2	123	0.63	0.87	31	HBX, MXN
3	151	0.62	0.84	31	HBX, MXN
4	68	0.41	0.80	17	empty

Interfaces

1 interface between chains.

A–B · 2036 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

5E4B · Hydroxynitrile lyase from the fern Davallia tyermanii in complex with (R)-mandelonitrile… · 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
Elsewhere: RCSB PDB 5E4B · PDBe 5E4B

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