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Apo structure of linalool dehydratase-isomerase

Analyse Apo structure of linalool dehydratase-isomerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5G1W
Type: protein
Length: 1,822 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Linalool DEHYDRATASE/ISOMERASE
EC: 4.2.1.127, 5.4.4.4
UniProt: E1XUJ2
Ligands: DXX
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Linalool DEHYDRATASE/ISOMERASE (EC 4.2.1.127, 5.4.4.4)	protein	364	57% helix, 7% strand	E1XUJ2
C, E	Linalool DEHYDRATASE/ISOMERASE (EC 4.2.1.127, 5.4.4.4)	protein	365	56% helix, 8% strand	E1XUJ2

Ligands and binding sites

DXX · Methylmalonic acid · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D, E

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

Pockets

12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	195	0.71	0.88	42	empty
2	175	0.70	0.88	32	empty
3	54	0.70	0.97	21	empty
4	159	0.68	0.87	33	empty
5	189	0.66	0.85	33	empty

Interfaces

5 interfaces between chains.

A–D · 1200 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 1191 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1188 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1184 Å² buried · 12 hydrogen bonds · protein-protein
C–E · 1175 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5G1W · Apo Structure of Linalool Dehydratase-Isomerase · the same entry in another collection · chain B against B, TM-score 1.00
E1XUJ2 · AlphaFold monomer V2.0 prediction for linalool DEHYDRATASE/ISOMERASE (E1XUJ2) · a predicted model of the same protein · 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 E1XUJ2
Elsewhere: RCSB PDB 5G1W · PDBe 5G1W · UniProt E1XUJ2

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