Research workbench

Canavalia gladiata lectin complexed with MAN1-3MAN-ome

Analyse Canavalia gladiata lectin complexed with MAN1-3MAN-ome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EF6
Type: protein
Length: 936 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin a
UniProt: P14894
Ligands: MMA, MAN, CA, MN
Pockets: 2 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Concanavalin a	protein	234	4% helix, 47% strand	P14894
B, D	Concanavalin a	protein	234	4% helix, 45% strand	P14894

Ligands and binding sites

MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B, C, D
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1116	0.84	0.85	115	empty
2	53	0.32	0.77	18	empty

Interfaces

5 interfaces between chains.

A–B · 1078 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1057 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 989 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 913 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 21 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2EF6 · Canavalia gladiata lectin complexed with Man1-3Man-OMe · the same entry in another collection · chain D against D, TM-score 1.00
P14894 · AlphaFold monomer V2.0 prediction for concanavalin-a (P14894) · a predicted model of the same protein · chain C against A, TM-score 0.51

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 P14894
Elsewhere: RCSB PDB 2EF6 · PDBe 2EF6 · UniProt P14894

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.