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Hydroxynitrile lyase from the fern davallia tyermanii in complex with benzoic acid

Analyse Hydroxynitrile lyase from the fern davallia tyermanii in complex with benzoic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E4D
Type: protein
Length: 351 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydroxynitrile lyase
Ligands: BEZ
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hydroxynitrile lyase	protein	175	28% helix, 38% strand	—
B	Hydroxynitrile lyase	protein	176	28% helix, 39% strand	—

Ligands and binding sites

BEZ · Benzoic acid · ligand · 4 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	246	0.67	0.84	41	BEZ
2	138	0.64	0.86	30	BEZ
3	124	0.64	0.87	29	BEZ
4	55	0.35	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 1994 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

5E4D · Hydroxynitrile lyase from the fern Davallia tyermanii in complex with benzoic acid · 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 5E4D · PDBe 5E4D

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