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Linalool dehydratase isomerase in complex with myrcene

Analyse Linalool dehydratase isomerase in complex with myrcene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TFN
Type: protein
Length: 3,626 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Linalool dehydratase-isomerase protein ldi
UniProt: W8X534
Ligands: N6Q
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 57% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Linalool dehydratase-isomerase protein ldi	protein	362	57% helix, 7% strand	W8X534
D, F	Linalool dehydratase-isomerase protein ldi	protein	361	57% helix, 7% strand	W8X534
E, G, J	Linalool dehydratase-isomerase protein ldi	protein	364	57% helix, 7% strand	W8X534
H, I	Linalool dehydratase-isomerase protein ldi	protein	363	57% helix, 7% strand	W8X534

Ligands and binding sites

N6Q · 7-methyl-3-methylidene-oct-1-ene · ligand · 6 copies · chains A, D, F, G, H, J, I

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	161	0.70	0.88	32	empty
2	149	0.68	0.88	33	N6Q
3	119	0.66	0.88	26	N6Q
4	125	0.66	0.88	25	N6Q
5	119	0.65	0.87	26	N6Q

Interfaces

11 interfaces between chains.

I–J · 1232 Å² buried · 11 hydrogen bonds · protein-protein
F–I · 1219 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1213 Å² buried · 11 hydrogen bonds · protein-protein
F–G · 1211 Å² buried · 15 hydrogen bonds · protein-protein
H–J · 1202 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6TFN · Linalool Dehydratase Isomerase in complex with Myrcene · 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 W8X534
Elsewhere: RCSB PDB 6TFN · PDBe 6TFN · UniProt W8X534

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