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Refined crystal structure of canavalin from jack bean

Analyse Refined crystal structure of canavalin from jack bean in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DGR
Type: protein
Length: 1,039 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Canavalin
UniProt: P50477
Ligands: PO4
Pockets: 15 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 16% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Canavalin	protein	178	17% helix, 42% strand	P50477
X	Canavalin	protein	75	8% helix, 55% strand	P50477
Y, W	Canavalin	protein	93	23% helix, 33% strand	P50477
V, N	Canavalin	protein	76	8% helix, 55% strand	P50477
M	Canavalin	protein	92	23% helix, 35% strand	P50477

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains X, Y, V, W, N, M

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.74	1.00	13	PO4
2	53	0.72	0.99	13	PO4
3	50	0.71	0.98	12	PO4
4	105	0.60	0.86	24	empty
5	102	0.59	0.86	29	empty

Interfaces

18 interfaces between chains.

V–W · 3566 Å² buried · 90 hydrogen bonds · protein-protein
N–M · 3553 Å² buried · 87 hydrogen bonds · protein-protein
X–Y · 3490 Å² buried · 86 hydrogen bonds · protein-protein
Y–C · 2066 Å² buried · 11 hydrogen bonds · protein-protein
A–W · 2043 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1DGR · Refined crystal structure of canavalin from jack bean · the same entry in another collection · chain M against M, TM-score 1.00
P50477 · AlphaFold monomer V2.0 prediction for canavalin (P50477) · a predicted model of the same protein · chain C 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 P50477
Elsewhere: RCSB PDB 1DGR · PDBe 1DGR · UniProt P50477

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