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The C2221 crystal form of canavalin at 173 K

Analyse The C2221 crystal form of canavalin at 173 K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V7J
Type: protein
Length: 1,055 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Canavalin
UniProt: P50477
Ligands: BEZ, CA
Pockets: 12 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Canavalin	protein	351	16% helix, 44% strand	P50477
B	Canavalin	protein	351	15% helix, 45% strand	P50477
C	Canavalin	protein	353	16% helix, 43% strand	P50477

Ligands and binding sites

BEZ · Benzoic acid · ligand · 3 copies · chains A, B, C
CA · Calcium ion · metal · 3 copies · chains A, C
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	57	0.74	0.99	15	BEZ
2	55	0.74	1.00	18	BEZ
3	56	0.74	0.99	14	BEZ
4	178	0.61	0.83	31	empty
5	123	0.58	0.84	31	empty

Interfaces

3 interfaces between chains.

A–B · 2763 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 2754 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 2736 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (oxidation).

Compared structures

6V7J · The C2221 crystal form of canavalin at 173 K · the same entry in another collection · chain A against A, 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 6V7J · PDBe 6V7J · UniProt P50477

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