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Frac with GLCNAC(6S) bound

Analyse Frac with GLCNAC(6S) bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GWF
Type: protein
Length: 708 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Delta-actitoxin-AFR1A
UniProt: B9W5G6
Ligands: NGY, CL
Pockets: 10 · 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	Delta-actitoxin-AFR1A	protein	177	13% helix, 47% strand	B9W5G6

Ligands and binding sites

NGY · 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose · ligand · 2 copies · chains B, D
CL · Chloride ion · ion · 13 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

10 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	209	0.60	0.82	34	CL
2	207	0.59	0.81	34	CL
3	139	0.56	0.83	24	CL, GOL
4	211	0.48	0.75	38	empty
5	146	0.44	0.76	21	empty

Interfaces

3 interfaces between chains.

C–D · 500 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 496 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 261 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5GWF · FraC with GlcNAc(6S) bound · 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 5GWF · PDBe 5GWF · UniProt B9W5G6

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