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The complex structure of SZ529 and expoxid

Analyse The complex structure of SZ529 and expoxid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YAO
Type: protein
Length: 263 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Limonene-1,2-epoxide hydrolase
EC: 3.3.2.8
UniProt: Q9ZAG3
Ligands: 3ZS, NA
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Limonene-1,2-epoxide hydrolase (EC 3.3.2.8)	protein	146	26% helix, 37% strand	Q9ZAG3
B	Limonene-1,2-epoxide hydrolase (EC 3.3.2.8)	protein	117	32% helix, 35% strand	Q9ZAG3

Ligands and binding sites

3ZS · (1R,5S)-6-oxabicyclo[3.1.0]hexane · ligand · chains A
NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

3 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	236	0.69	0.85	32	3ZS
2	226	0.64	0.82	21	empty
3	250	0.58	0.79	31	empty

Interfaces

1 interface between chains.

A–B · 179 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5YAO · The complex structure of SZ529 and expoxid · 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 Q9ZAG3
Elsewhere: RCSB PDB 5YAO · PDBe 5YAO · UniProt Q9ZAG3

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