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Concanavalin a bound to a DNA glycoconjugate, man-cgcg

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

PDB: 7MG8
Type: protein + DNA
Length: 473 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-a; DNA (5'-D(P*CP*GP*CP*G)-3')
UniProt: P02866
Ligands: SQ0, MAN, MN, CA
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Concanavalin-a	protein	233	4% helix, 48% strand	P02866
B	Concanavalin-a	protein	232	5% helix, 46% strand	P02866
C, D	DNA (5'-D(PCPGPCPG)-3')	dna	4	—	—

Ligands and binding sites

SQ0 · 3-{[2-(2-hydroxyethoxy)ethyl]amino}-4-[(6-hydroxyhexyl)amino]cyclobut-3-ene-1,2-dione · ligand · 2 copies · chains A, C, B, D
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.35	0.78	15	empty
2	74	0.34	0.76	14	empty

Interfaces

3 interfaces between chains.

A–B · 983 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 74 Å² buried · 1 hydrogen bond · protein-nucleic
A–C · 54 Å² buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7MG8 · Concanavalin A bound to a DNA glycoconjugate, Man-CGCG · the same entry in another collection · chain A against A, TM-score 1.00
P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain B 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 P02866
Elsewhere: RCSB PDB 7MG8 · PDBe 7MG8 · UniProt P02866

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