Research workbench

Concanavalin a bound to a DNA glycoconjugate, T(MAN-T)TT

Analyse Concanavalin a bound to a DNA glycoconjugate, T(MAN-T)TT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MGD
Type: protein
Length: 924 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-a
UniProt: P02866
Ligands: MMA, MN, CA
Pockets: 1 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Concanavalin-a	protein	231	5% helix, 44% strand	P02866

Ligands and binding sites

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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	934	0.85	0.86	103	empty

Interfaces

4 interfaces between chains.

B–C · 1068 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1060 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 688 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 655 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7MGD · Concanavalin A bound to a DNA glycoconjugate, T(Man-T)TT · the same entry in another collection · chain D against D, TM-score 1.00
P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain A against A, TM-score 0.52

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 P02866
Elsewhere: RCSB PDB 7MGD · PDBe 7MGD · UniProt P02866

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