MolNFT v1 · #82752 · protein

High resolution crystal structure of frac in the monomeric form

3VWI · Fragaceatoxin C: “High resolution crystal structure of frac in the monomeric form”. X-ray diffraction, 3 ligands (CL, NH4, SO4), 9 pockets (best druggability 0.60). MolNFT v1 #82752 on GenesisL1: 3D structure, binding sites and…

PDB: 3VWI
Type: protein
Length: 708 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fragaceatoxin C
UniProt: B9W5G6
Ligands: CL, NH4, SO4
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 47% strand (DSSP).

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

Ligands and binding sites

CL · Chloride ion · ion · 8 copies · chains A, B, C, D
NH4 · Ammonium ion · ion · 2 copies
SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains B, C

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

Pockets

9 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	197	0.60	0.82	34	CL
2	225	0.60	0.81	38	CL
3	142	0.56	0.82	26	CL, GOL
4	189	0.46	0.75	29	empty
5	141	0.42	0.75	24	empty

Interfaces

3 interfaces between chains.

A–B · 479 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 472 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 262 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3VWI · High resolution crystal structure of FraC in the monomeric form · 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 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 B9W5G6
Elsewhere: RCSB PDB 3VWI · PDBe 3VWI · UniProt B9W5G6

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