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N225D trichodiene synthase

Analyse N225D trichodiene synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PS4
Type: protein
Length: 704 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trichodiene synthase
EC: 4.2.3.6
UniProt: P13513
Ligands: MG
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trichodiene synthase (EC 4.2.3.6)	protein	354	72% helix, 0% strand	P13513
B	Trichodiene synthase (EC 4.2.3.6)	protein	350	68% helix, 0% strand	P13513

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 4 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	578	0.77	0.84	53	MG, EDO
2	95	0.76	0.98	19	empty
3	504	0.76	0.84	51	EDO
4	67	0.74	0.98	20	EDO
5	119	0.64	0.87	25	empty

Interfaces

1 interface between chains.

A–B · 2735 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2PS4 · N225D 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 2PS4 · PDBe 2PS4 · UniProt P13513

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