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Crystal structure of AaTPS with PPi

Analyse Crystal structure of AaTPS with PPi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LCD
Type: protein
Length: 745 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.7
Source: Alternaria alternata
Molecule: AaTPS
Ligands: FPP, MG
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · resolution 2.7 · 2 distinct chains · 61% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AaTPS	protein	373	61% helix, 3% strand	—
B	AaTPS	protein	372	61% helix, 3% strand	—

Ligands and binding sites

FPP · Farnesyl diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	880	0.80	0.82	71	FPP, MG
2	825	0.76	0.80	53	FPP, MG
3	59	0.50	0.86	14	empty
4	199	0.48	0.76	28	empty
5	50	0.45	0.84	14	empty

Interfaces

1 interface between chains.

A–B · 711 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6LCD · Crystal structure of aatps with ppi · 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
Elsewhere: RCSB PDB 6LCD · PDBe 6LCD

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