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Crystal structure of procruciferin, 11S globulin from brassica napus

Analyse Crystal structure of procruciferin, 11S globulin from brassica napus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KGL
Type: protein
Length: 2,347 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cruciferin
UniProt: Q7XB53
Ligands: SO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 12% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cruciferin	protein	398	13% helix, 39% strand	Q7XB53
B	Cruciferin	protein	387	13% helix, 37% strand	Q7XB53
C	Cruciferin	protein	387	12% helix, 37% strand	Q7XB53
D	Cruciferin	protein	390	12% helix, 38% strand	Q7XB53
E	Cruciferin	protein	389	13% helix, 37% strand	Q7XB53
F	Cruciferin	protein	396	13% helix, 38% strand	Q7XB53

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D, F, E
GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	749	0.80	0.84	80	empty
2	222	0.79	0.93	31	empty
3	238	0.78	0.92	48	empty
4	328	0.77	0.89	53	SO4
5	165	0.76	0.93	32	empty

Interfaces

12 interfaces between chains.

D–E · 2956 Å² buried · 62 hydrogen bonds · protein-protein
E–F · 2956 Å² buried · 56 hydrogen bonds · protein-protein
A–C · 2926 Å² buried · 56 hydrogen bonds · protein-protein
B–C · 2917 Å² buried · 49 hydrogen bonds · protein-protein
A–B · 2910 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3KGL · Crystal structure of procruciferin, 11S globulin from Brassica napus · 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
Every structure of UniProt Q7XB53
Elsewhere: RCSB PDB 3KGL · PDBe 3KGL · UniProt Q7XB53

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