Research workbench

D100E trichodiene synthase

Analyse D100E trichodiene synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KIY
Type: protein
Length: 708 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trichodiene synthase
EC: 4.1.99.6
UniProt: P13513
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Trichodiene synthase (EC 4.1.99.6)	protein	354	71% helix, 0% strand	P13513

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 6 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.78	0.98	21	empty
2	590	0.77	0.83	53	EDO
3	608	0.77	0.83	49	EDO
4	64	0.74	0.98	19	EDO
5	306	0.59	0.78	40	empty

Interfaces

1 interface between chains.

A–B · 2753 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

1KIY · D100E trichodiene synthase · the same entry in another collection · chain A against A, TM-score 1.00
P13513 · AlphaFold monomer V2.0 prediction for trichodiene synthase (P13513) · 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 P13513
Elsewhere: RCSB PDB 1KIY · PDBe 1KIY · UniProt P13513

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