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Crystal structure of frac with lipids

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

PDB: 4TSY
Type: protein
Length: 704 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fragaceatoxin C
UniProt: B9W5G6
Ligands: HXJ, HTO, SO4
Pockets: 8 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Fragaceatoxin C	protein	176	18% helix, 46% strand	B9W5G6

Ligands and binding sites

HXJ · 2-[[(E,2S,3R)-2-(hexanoylamino)-3-oxidanyl-dec-4-enoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium · ligand · 12 copies · chains A, B, C, D
HTO · Heptane-1,2,3-triol · ligand · chains A
SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	197	0.46	0.75	28	HXJ
2	204	0.46	0.74	31	HXJ
3	192	0.45	0.74	30	HXJ
4	66	0.35	0.77	16	HXJ
5	68	0.34	0.76	16	HXJ

Interfaces

3 interfaces between chains.

C–D · 818 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 799 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 798 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4TSY · Crystal structure of FraC with lipids · the same entry in another collection · chain D against D, TM-score 1.00
B9W5G6 · AlphaFold monomer V2.0 prediction for delta-actitoxin-AFR1A (B9W5G6) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 B9W5G6
Elsewhere: RCSB PDB 4TSY · PDBe 4TSY · UniProt B9W5G6

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