MolNFT v1 · #106869 · protein

Crystal structure of frac with poc bound (crystal form II)

4TSN · Fragaceatoxin C: “Crystal structure of frac with poc bound (crystal form II)”. X-ray diffraction, 2 ligands (PC, SO4), 10 pockets (best druggability 0.61). MolNFT v1 #106869 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4TSN
Type: protein
Length: 711 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fragaceatoxin C
UniProt: B9W5G6
Ligands: PC, SO4
Pockets: 10 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Fragaceatoxin C	protein	178	13% helix, 47% strand	B9W5G6
C	Fragaceatoxin C	protein	177	12% helix, 47% strand	B9W5G6

Ligands and binding sites

PC · Phosphocholine · ligand · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 12 copies · chains A, B, D, C
ACT · Acetate ion · additive · 2 copies · chains B, D
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.61	0.86	31	empty
2	150	0.47	0.77	23	empty
3	147	0.47	0.77	21	empty
4	149	0.38	0.73	26	SO4
5	102	0.38	0.75	20	empty

Interfaces

4 interfaces between chains.

A–C · 752 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 534 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 48 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 29 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4TSN · Crystal structure of FraC with POC bound (crystal form II) · 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 B against A, TM-score 0.99

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 4TSN · PDBe 4TSN · UniProt B9W5G6

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