MolNFT v1 · #48405 · protein

Y295F trichodiene synthase: complex with mg and pyrophosphate

2PS8: “Y295F trichodiene synthase: complex with mg and pyrophosphate”. X-ray diffraction, 2 ligands (POP, MG), 12 pockets (best druggability 0.82). MolNFT v1 #48405 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PS8
Type: protein
Length: 708 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: POP, MG
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Trichodiene synthase (EC 4.2.3.6)	protein	354	70% helix, 0% strand	P13513

Ligands and binding sites

POP · Pyrophosphate 2- · ligand · chains B
MG · Magnesium ion · metal · 3 copies · chains B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	181	0.82	0.97	35	MG, POP
2	632	0.78	0.83	51	empty
3	90	0.77	0.98	18	empty
4	75	0.76	0.98	20	EDO
5	324	0.62	0.79	40	empty

Interfaces

1 interface between chains.

A–B · 2760 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

2PS8 · Y295F Trichodiene Synthase: Complex With Mg and Pyrophosphate · 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 2PS8 · PDBe 2PS8 · UniProt P13513

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